Marine Life Science & Technology最新文献

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Response of Salmonella enterica serovar Typhimurium to alginate oligosaccharides fermented with fecal inoculum: integrated transcriptomic and metabolomic analyses. 鼠伤寒血清型肠炎沙门氏菌对用粪便接种物发酵的藻酸盐低聚糖的反应:综合转录组学和代谢组学分析。
IF 5.7 2区 生物学
Marine Life Science & Technology Pub Date : 2023-05-29 eCollection Date: 2023-05-01 DOI: 10.1007/s42995-023-00176-z
Jiaying Cheng, Mengshi Xiao, Xinmiao Ren, Francesco Secundo, Ying Yu, Shihao Nan, Weimiao Chen, Changliang Zhu, Qing Kong, Youtao Huang, Xiaodan Fu, Haijin Mou
{"title":"Response of <i>Salmonella enterica</i> serovar Typhimurium to alginate oligosaccharides fermented with fecal inoculum: integrated transcriptomic and metabolomic analyses.","authors":"Jiaying Cheng,&nbsp;Mengshi Xiao,&nbsp;Xinmiao Ren,&nbsp;Francesco Secundo,&nbsp;Ying Yu,&nbsp;Shihao Nan,&nbsp;Weimiao Chen,&nbsp;Changliang Zhu,&nbsp;Qing Kong,&nbsp;Youtao Huang,&nbsp;Xiaodan Fu,&nbsp;Haijin Mou","doi":"10.1007/s42995-023-00176-z","DOIUrl":"10.1007/s42995-023-00176-z","url":null,"abstract":"<p><p>Alginate oligosaccharides (AOS), extracted from marine brown algae, are a common functional feed additive; however, it remains unclear whether they modulate the gut microbiota and microbial metabolites. The response of <i>Salmonella enterica</i> serovar Typhimurium, a common poultry pathogen, to AOS fermented with chicken fecal inocula was investigated using metabolomic and transcriptomic analyses. Single-strain cultivation tests showed that AOS did not directly inhibit the growth of <i>S</i>. Typhimurium. However, when AOS were fermented by chicken fecal microbiota, the supernatant of fermented AOS (F-AOS) exhibited remarkable antibacterial activity against <i>S</i>. Typhimurium, decreasing the abundance ratio of <i>S</i>. Typhimurium in the fecal microbiota from 18.94 to 2.94%. Transcriptomic analyses showed that the 855 differentially expressed genes induced by F-AOS were mainly enriched in porphyrin and chlorophyll metabolism, oxidative phosphorylation, and <i>Salmonella</i> infection-related pathways. RT-qPCR confirmed that F-AOS downregulated key genes involved in flagellar assembly and the type III secretory system of <i>S</i>. Typhimurium, indicating metabolites in F-AOS can influence the growth and metabolism of <i>S</i>. Typhimurium. Metabolomic analyses showed that 205 microbial metabolites were significantly altered in F-AOS. Among them, the increase in indolelactic acid and 3-indolepropionic acid levels were further confirmed using HPLC. This study provides a new perspective for the application of AOS as a feed additive against pathogenic intestinal bacteria.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s42995-023-00176-z.</p>","PeriodicalId":53218,"journal":{"name":"Marine Life Science & Technology","volume":"5 2","pages":"242-256"},"PeriodicalIF":5.7,"publicationDate":"2023-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10232696/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9587932","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Comparative genome analysis of three euplotid protists provides insights into the evolution of nanochromosomes in unicellular eukaryotic organisms. 对三种真仆虫原生生物的比较基因组分析为单细胞真核生物中纳米染色体的进化提供了见解。
IF 5.8 2区 生物学
Marine Life Science & Technology Pub Date : 2023-05-28 eCollection Date: 2023-08-01 DOI: 10.1007/s42995-023-00175-0
Didi Jin, Chao Li, Xiao Chen, Adam Byerly, Naomi A Stover, Tengteng Zhang, Chen Shao, Yurui Wang
{"title":"Comparative genome analysis of three euplotid protists provides insights into the evolution of nanochromosomes in unicellular eukaryotic organisms.","authors":"Didi Jin, Chao Li, Xiao Chen, Adam Byerly, Naomi A Stover, Tengteng Zhang, Chen Shao, Yurui Wang","doi":"10.1007/s42995-023-00175-0","DOIUrl":"10.1007/s42995-023-00175-0","url":null,"abstract":"<p><p>One of the most diverse clades of ciliated protozoa, the class Spirotrichea, displays a series of unique characters in terms of eukaryotic macronuclear (MAC) genome, including high fragmentation that produces nanochromosomes. However, the genomic diversity and evolution of nanochromosomes and gene families for spirotrich MAC genomes are poorly understood. In this study, we assemble the MAC genome of a representative euplotid (a new model organism in Spirotrichea) species, <i>Euplotes aediculatus</i>. Our results indicate that: (a) the MAC genome includes 35,465 contigs with a total length of 97.3 Mb and a contig N50 of 3.4 kb, and contains 13,145 complete nanochromosomes and 43,194 predicted genes, with the majority of these nanochromosomes containing tiny introns and harboring only one gene; (b) genomic comparisons between <i>E. aediculatus</i> and other reported spirotrichs indicate that average GC content and genome fragmentation levels exhibit interspecific variation, and chromosome breaking sites (CBSs) might be lost during evolution, resulting in the increase of multi-gene nanochromosome; (c) gene families associated with chitin metabolism and FoxO signaling pathway are expanded in <i>E. aediculatus</i>, suggesting their potential roles in environment adaptation and survival strategies of <i>E. aediculatus</i>; and (d) a programmed ribosomal frameshift (PRF) with a conservative motif 5'-AAATAR-3' tends to occur in longer genes with more exons, and PRF genes play an important role in many cellular regulation processes.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s42995-023-00175-0.</p>","PeriodicalId":53218,"journal":{"name":"Marine Life Science & Technology","volume":"5 3","pages":"300-315"},"PeriodicalIF":5.8,"publicationDate":"2023-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10449743/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10110063","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Isolation and characterization of three pairs of verrucosidin epimers from the marine sediment-derived fungus Penicillium cyclopium and configuration revision of penicyrone A and related analogues. 从海洋沉积物来源的真菌环青霉中分离、鉴定三对疣苷差向异构体,并对青霉烯酮A及其类似物进行结构修饰。
IF 5.7 2区 生物学
Marine Life Science & Technology Pub Date : 2023-05-28 eCollection Date: 2023-05-01 DOI: 10.1007/s42995-023-00173-2
Yan-He Li, Attila Mándi, Hong-Lei Li, Xiao-Ming Li, Xin Li, Ling-Hong Meng, Sui-Qun Yang, Xiao-Shan Shi, Tibor Kurtán, Bin-Gui Wang
{"title":"Isolation and characterization of three pairs of verrucosidin epimers from the marine sediment-derived fungus <i>Penicillium cyclopium</i> and configuration revision of penicyrone A and related analogues.","authors":"Yan-He Li,&nbsp;Attila Mándi,&nbsp;Hong-Lei Li,&nbsp;Xiao-Ming Li,&nbsp;Xin Li,&nbsp;Ling-Hong Meng,&nbsp;Sui-Qun Yang,&nbsp;Xiao-Shan Shi,&nbsp;Tibor Kurtán,&nbsp;Bin-Gui Wang","doi":"10.1007/s42995-023-00173-2","DOIUrl":"10.1007/s42995-023-00173-2","url":null,"abstract":"<p><p>Verrucosidins, a methylated α-pyrone class of polyketides rarely reported upon, have been implicated in one or more neurological diseases. Despite the significance of verrucosidins as neurotoxins, the absolute configurations of most of the derivatives have not been accurately characterized yet. In this study, three pairs of C-9 epimeric verrucosidin derivatives, including the known compounds penicyrones A and B (<b>1a/1b</b>) and 9-<i>O</i>-methylpenicyrones A and B (<b>2a/2b</b>), the new compounds 9-<i>O-</i>ethylpenicyrones A and B (<b>3a/3b</b>), together with the related known derivative verrucosidin (<b>4</b>), were isolated and identified from the culture extract of <i>Penicillium cyclopium</i> SD-413, which was obtained from the marine sediment collected from the East China sea. Their structures were established based on an in-depth analysis of nuclear magnetic resonances (NMR) and mass spectroscopic data. Determination of the absolute configurations of these compounds was accomplished by Mosher's method and time-dependent density functional theory (TDDFT) calculations of electronic circular dichroism (ECD) and optical rotation (OR). The configurational assignment of penicyrone A demonstrated that the previously reported C-6 absolute configuration of verrucosidin derivatives needs to be revised from (6<i>S</i>) to (6<i>R</i>). The 9<i>R</i>/9<i>S</i> epimers of compounds <b>1-3</b> were found to exhibit growth inhibition against some pathogenic bacteria, indicating that they have potential as lead compounds for the creation of antimicrobial agents.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s42995-023-00173-2.</p>","PeriodicalId":53218,"journal":{"name":"Marine Life Science & Technology","volume":"5 2","pages":"223-231"},"PeriodicalIF":5.7,"publicationDate":"2023-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10232390/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9939878","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Expansion and adaptive evolution of the WRKY transcription factor family in Avicennia mangrove trees. 阿维森尼亚红树林WRKY转录因子家族的扩展和适应性进化。
IF 5.7 2区 生物学
Marine Life Science & Technology Pub Date : 2023-05-23 eCollection Date: 2023-05-01 DOI: 10.1007/s42995-023-00177-y
Xiao Feng, Guohong Li, Weihong Wu, Haomin Lyu, Jiexin Wang, Cong Liu, Cairong Zhong, Suhua Shi, Ziwen He
{"title":"Expansion and adaptive evolution of the <i>WRKY</i> transcription factor family in <i>Avicennia</i> mangrove trees.","authors":"Xiao Feng,&nbsp;Guohong Li,&nbsp;Weihong Wu,&nbsp;Haomin Lyu,&nbsp;Jiexin Wang,&nbsp;Cong Liu,&nbsp;Cairong Zhong,&nbsp;Suhua Shi,&nbsp;Ziwen He","doi":"10.1007/s42995-023-00177-y","DOIUrl":"10.1007/s42995-023-00177-y","url":null,"abstract":"<p><p>Mangroves are adapted to intertidal zones, which present extreme environmental conditions. WRKYs are among the most prominent transcription factors (TFs) in higher plants and act through various interconnected networks to regulate responses to multiple abiotic stressors. Here, based on omic data, we investigated the landscape and evolutionary patterns of WRKYs in the main mangrove genus <i>Avicennia</i>. We found that both the number and the proportion of TFs and WRKYs in <i>Avicennia</i> species exceeded their inland relatives, indicating a significant expansion of WRKYs in <i>Avicennia</i>. We identified 109 <i>WRKY</i> genes in the representative species <i>Avicennia marina</i>. Comparative genomic analysis showed that two recent whole-genome duplication (WGD) events played a critical role in the expansion of <i>WRKY</i>s, and 88% of <i>Avicennia marina WRKY</i>s (<i>AmWRKY</i>s) have been retained following these WGDs. Applying comparative transcriptomics on roots under experimental salt gradients, we inferred that there is high divergence in the expression of WGD-retained <i>AmWRKY</i>s. Moreover, we found that the expression of 16 <i>AmWRKY</i>s was stable between freshwater and moderately saline water but increased when the trees were exposed to high salinity. In particular, 14 duplicates were retained following the two recent WGD events, indicating potential neo- and sub-functionalization. We also found that WRKYs could interact with other upregulated genes involved in signalling pathways and natural antioxidant biosynthesis to enhance salt tolerance, contributing to the adaptation to intertidal zones. Our omic data of the WRKY family in <i>A. marina</i> broadens the understanding of how a TF family relates to the adaptive evolution of mangroves.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s42995-023-00177-y.</p>","PeriodicalId":53218,"journal":{"name":"Marine Life Science & Technology","volume":"5 2","pages":"155-168"},"PeriodicalIF":5.7,"publicationDate":"2023-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10232687/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9637370","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
The neuroprotective effects of peracetylated chitosan oligosaccharides against β-amyloid-induced cognitive deficits in rats. 过乙酰壳聚糖寡糖对β-淀粉样蛋白诱导的大鼠认知缺陷的神经保护作用。
IF 5.7 2区 生物学
Marine Life Science & Technology Pub Date : 2023-05-22 eCollection Date: 2023-05-01 DOI: 10.1007/s42995-023-00172-3
Cui Hao, Minmin Han, Wei Wang, Cheng Yang, Jigang Wang, Yunliang Guo, Tao Xu, Lijuan Zhang, Chunxia Li
{"title":"The neuroprotective effects of peracetylated chitosan oligosaccharides against β-amyloid-induced cognitive deficits in rats.","authors":"Cui Hao, Minmin Han, Wei Wang, Cheng Yang, Jigang Wang, Yunliang Guo, Tao Xu, Lijuan Zhang, Chunxia Li","doi":"10.1007/s42995-023-00172-3","DOIUrl":"10.1007/s42995-023-00172-3","url":null,"abstract":"<p><p>Chitosan oligosaccharides (COSs) have been reported to possess a broad range of activities such as antitumor, antioxidant and neuroprotective activities. In this study, the protective effects and mechanisms of peracetylated chitosan oligosaccharides (PACOs) against Aβ-induced cognitive deficits were investigated in Sprague-Dawley (SD) rats. PACOs treatment significantly improved the learning and memory function of Alzheimer's disease (AD) rats and attenuated the neuron cell damage caused by Aβ. PACOs also markedly reduced the levels of lactate dehydrogenase (LDH) and Malondialdehyde (MDA) and decreased the phosphorylation of Tau protein to inhibit oxidative injury and inflammatory responses in AD rats. Further studies indicated that PACOs may promote the repair of Aβ induced nerve damage and inhibit neuronal apoptosis mainly through regulating PI3K/Akt/GSK3β signaling pathway. Consistently, the transcriptome analysis verified that the differentially expressed genes (DEGs) were mainly involved in neuron development and the PI3K-Akt signaling pathway. Taken together, peracetylated chitosan oligosaccharides (PACOs) have the potential to be developed into novel anti-AD agents targeting the cellular PI3K/Akt/GSK3β signaling pathway.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s42995-023-00172-3.</p>","PeriodicalId":53218,"journal":{"name":"Marine Life Science & Technology","volume":"5 2","pages":"211-222"},"PeriodicalIF":5.7,"publicationDate":"2023-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10232394/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9939880","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Colonization-competition dynamics of basal species shape food web complexity in island metacommunities. 基础物种的定居竞争动态塑造了岛屿元群落中食物网的复杂性。
IF 5.7 2区 生物学
Marine Life Science & Technology Pub Date : 2023-05-09 eCollection Date: 2023-05-01 DOI: 10.1007/s42995-023-00167-0
Guanming Guo, Fei Zhao, Ivan Nijs, Jinbao Liao
{"title":"Colonization-competition dynamics of basal species shape food web complexity in island metacommunities.","authors":"Guanming Guo,&nbsp;Fei Zhao,&nbsp;Ivan Nijs,&nbsp;Jinbao Liao","doi":"10.1007/s42995-023-00167-0","DOIUrl":"10.1007/s42995-023-00167-0","url":null,"abstract":"<p><p>Exploring how food web complexity emerges and evolves in island ecosystems remains a major challenge in ecology. Food webs assembled from multiple islands are commonly recognized as highly complex trophic networks that are dynamic in both space and time. In the context of global climate change, it remains unclear whether food web complexity will decrease in a monotonic fashion when undergoing habitat destruction (e.g., the inundation of islands due to sea-level rise). Here, we develop a simple yet comprehensive patch-dynamic framework for complex food web metacommunities subject to the competition-colonization tradeoff between basal species. We found that oscillations in food web topological complexity (characterized by species diversity, mean food chain length and the degree of omnivory) emerge along the habitat destruction gradient. This outcome is robust to changing parameters or relaxing the assumption of a strict competitive hierarchy. Having oscillations in food web complexity indicates that small habitat changes could have disproportionate negative effects on species diversity, thus the success of conservation actions should be evaluated not only on changes in biodiversity, but also on system robustness to habitat alteration. Overall, this study provides a parsimonious mechanistic explanation for the emergence of food web complexity in island ecosystems, further enriching our understanding of metacommunity assembly.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s42995-023-00167-0.</p>","PeriodicalId":53218,"journal":{"name":"Marine Life Science & Technology","volume":"5 2","pages":"169-177"},"PeriodicalIF":5.7,"publicationDate":"2023-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10232389/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9637819","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Discovery of a natural small-molecule AMP-activated kinase activator that alleviates nonalcoholic steatohepatitis. 发现一种天然小分子AMP活化激酶激活剂,可缓解非酒精性脂肪性肝炎。
IF 5.7 2区 生物学
Marine Life Science & Technology Pub Date : 2023-04-30 eCollection Date: 2023-05-01 DOI: 10.1007/s42995-023-00168-z
Jin Chen, Li Xu, Xue-Qing Zhang, Xue Liu, Zi-Xuan Zhang, Qiu-Mei Zhu, Jian-Yu Liu, Muhammad Omer Iqbal, Ning Ding, Chang-Lun Shao, Mei-Yan Wei, Yu-Chao Gu
{"title":"Discovery of a natural small-molecule AMP-activated kinase activator that alleviates nonalcoholic steatohepatitis.","authors":"Jin Chen,&nbsp;Li Xu,&nbsp;Xue-Qing Zhang,&nbsp;Xue Liu,&nbsp;Zi-Xuan Zhang,&nbsp;Qiu-Mei Zhu,&nbsp;Jian-Yu Liu,&nbsp;Muhammad Omer Iqbal,&nbsp;Ning Ding,&nbsp;Chang-Lun Shao,&nbsp;Mei-Yan Wei,&nbsp;Yu-Chao Gu","doi":"10.1007/s42995-023-00168-z","DOIUrl":"10.1007/s42995-023-00168-z","url":null,"abstract":"<p><p>Non-alcoholic steatohepatitis (NASH) is a primary cause of cirrhosis and hepatocellular carcinoma. Unfortunately, there is no approved drug treatment for NASH. AMP-activated kinase (AMPK) is an important metabolic sensor and whole-body regulator. It has been proposed that AMPK activators could be used for treating metabolic diseases such as obesity, type 2 diabetes and NASH. In this study, we screened a marine natural compound library by monitoring AMPK activity and found a potent AMPK activator, candidusin A (<b>CHNQD-0803</b>). Further studies showed that <b>CHNQD-0803</b> directly binds recombinant AMPK with a <i>K</i><sub>D</sub> value of 4.728 × 10<sup>-8</sup> M and activates AMPK at both molecular and intracellular levels. We then investigated the roles and mechanisms of <b>CHNQD-0803</b> in PA-induced fat deposition, LPS-stimulated inflammation, TGF-β-induced fibrosis cell models and the MCD-induced mouse model of NASH. The results showed that <b>CHNQD-0803</b> inhibited the expression of adipogenesis genes and reduced fat deposition, negatively regulated the NF-κB-TNFα inflammatory axis to suppress inflammation, and ameliorated liver injury and fibrosis. These data indicate that <b>CHNQD-0803</b> as an AMPK activator is a novel potential therapeutic candidate for NASH treatment.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s42995-023-00168-z.</p>","PeriodicalId":53218,"journal":{"name":"Marine Life Science & Technology","volume":"5 2","pages":"196-210"},"PeriodicalIF":5.7,"publicationDate":"2023-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10232707/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9637820","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Phylotype resolved spatial variation and association patterns of planktonic Thaumarchaeota in eastern Chinese marginal seas. 系统发育类型解析了中国东部边缘海域浮游Thaumarchaeota的空间变异和组合模式。
IF 5.7 2区 生物学
Marine Life Science & Technology Pub Date : 2023-04-07 eCollection Date: 2023-05-01 DOI: 10.1007/s42995-023-00169-y
Jiwen Liu, Fuyan Huang, Jiao Liu, Xiaoyue Liu, Ruiyun Lin, Xiaosong Zhong, Brian Austin, Xiao-Hua Zhang
{"title":"Phylotype resolved spatial variation and association patterns of planktonic <i>Thaumarchaeota</i> in eastern Chinese marginal seas.","authors":"Jiwen Liu,&nbsp;Fuyan Huang,&nbsp;Jiao Liu,&nbsp;Xiaoyue Liu,&nbsp;Ruiyun Lin,&nbsp;Xiaosong Zhong,&nbsp;Brian Austin,&nbsp;Xiao-Hua Zhang","doi":"10.1007/s42995-023-00169-y","DOIUrl":"10.1007/s42995-023-00169-y","url":null,"abstract":"<p><p>The majority of marine ammonia oxidizers belong to <i>Thaumarchaeota</i>, a phylum of Archaea, which is distributed throughout the water column. Marine surface waters contain distinct thaumarchaeotal phylotypes compared to the deeper ocean, but spatial dynamics of the surface-associated lineages are largely unsolved. This study of 120 seawater samples from the eastern Chinese marginal seas identified contrasting distribution and association patterns among thaumarchaeotal phylotypes across different dimensions. Horizontally, <i>Nitrosopumilus</i>-like and <i>Nitrosopelagicus</i>-like phylotypes dominated the surface water (3 m) of the Yellow Sea (YS) and East China Sea (ECS), respectively, along with increased abundance of total free-living <i>Thaumarchaeota</i> in ECS. Similar compositional changes were observed in the surface microlayer. The spatial heterogeneity of particle-attached <i>Thaumarchaeota</i> was less clear in surface microlayers than in surface waters. Vertically, the <i>Nitrosopelagicus</i>-like phylotype increased in abundance from surface to 90 m in ECS, which led to an increase in the proportion of <i>Thaumarchaeota</i> relative to total prokaryotes. This occurred mainly in the free-living fraction. These results indicate a clear size-fractionated niche partitioning, which is more pronounced at lower depths than in the surface water/surface microlayer. In addition, associations of <i>Thaumarchaeota</i> with other microbial taxa varied between phylotypes and size fractions. Our results show that a phylotype-resolved and size-fractionated spatial heterogeneity of the thaumarchaeotal community is present in surface oceanic waters and a vertical variation of the <i>Nitrosopelagicus</i>-like phylotype is present in shallow shelf waters.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s42995-023-00169-y.</p>","PeriodicalId":53218,"journal":{"name":"Marine Life Science & Technology","volume":"5 2","pages":"257-270"},"PeriodicalIF":5.7,"publicationDate":"2023-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10232715/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9637369","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Population structure and genome-wide evolutionary signatures reveal putative climate-driven habitat change and local adaptation in the large yellow croaker. 种群结构和全基因组进化特征揭示了气候驱动的大黄鱼栖息地变化和局部适应。
IF 5.7 2区 生物学
Marine Life Science & Technology Pub Date : 2023-04-07 eCollection Date: 2023-05-01 DOI: 10.1007/s42995-023-00165-2
Baohua Chen, Yulin Bai, Jiaying Wang, Qiaozhen Ke, Zhixiong Zhou, Tao Zhou, Ying Pan, Renxie Wu, Xiongfei Wu, Weiqiang Zheng, Peng Xu
{"title":"Population structure and genome-wide evolutionary signatures reveal putative climate-driven habitat change and local adaptation in the large yellow croaker.","authors":"Baohua Chen,&nbsp;Yulin Bai,&nbsp;Jiaying Wang,&nbsp;Qiaozhen Ke,&nbsp;Zhixiong Zhou,&nbsp;Tao Zhou,&nbsp;Ying Pan,&nbsp;Renxie Wu,&nbsp;Xiongfei Wu,&nbsp;Weiqiang Zheng,&nbsp;Peng Xu","doi":"10.1007/s42995-023-00165-2","DOIUrl":"10.1007/s42995-023-00165-2","url":null,"abstract":"<p><p>The large yellow croaker (<i>Larimichthys</i> <i>crocea</i>) is one of the most economically valuable marine fish in China and is a notable species in ecological studies owing to a serious collapse of wild germplasm in the past few decades. The stock division and species distribution, which have important implications for ecological protection, germplasm recovery, and fishery resource management, have been debated since the 1960s. However, it is still uncertain even how many stocks exist in this species. To address this, we evaluated the fine-scale genetic structure of large yellow croaker populations distributed along the eastern and southern Chinese coastline based on 7.64 million SNP markers. Compared with the widely accepted stock boundaries proposed in the 1960s, our results revealed that a climate-driven habitat change probably occurred between the Naozhou (Nanhai) Stock and the Ming-Yuedong (Mindong) Stock. The boundary between these two stocks might have shifted northwards from the Pearl River Estuary to the northern area of the Taiwan Strait, accompanied by highly asymmetric introgression. In addition, we found divergent landscapes of natural selection between the stocks inhabiting northern and southern areas. The northern population exhibited highly agminated signatures of strong natural selection in genes related to developmental processes, whereas moderate and interspersed selective signatures were detected in many immune-related genes in the southern populations. These findings establish the stock status and genome-wide evolutionary landscapes of large yellow croaker, providing a basis for conservation, fisheries management and further evolutionary biology studies.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s42995-023-00165-2.</p>","PeriodicalId":53218,"journal":{"name":"Marine Life Science & Technology","volume":"5 2","pages":"141-154"},"PeriodicalIF":5.7,"publicationDate":"2023-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10232709/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9637818","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Correction: Genomic diversity and ecological distribution of marine Pseudoalteromonas phages. 更正:海洋拟交替单胞菌噬菌体的基因组多样性和生态分布。
IF 5.7 2区 生物学
Marine Life Science & Technology Pub Date : 2023-04-07 eCollection Date: 2023-05-01 DOI: 10.1007/s42995-023-00166-1
Kaiyang Zheng, Yue Dong, Yantao Liang, Yundan Liu, Xinran Zhang, Wenjing Zhang, Ziyue Wang, Hongbing Shao, Yeong Yik Sung, Wen Jye Mok, Li Lian Wong, Andrew McMinn, Min Wang
{"title":"Correction: Genomic diversity and ecological distribution of marine <i>Pseudoalteromonas</i> phages.","authors":"Kaiyang Zheng,&nbsp;Yue Dong,&nbsp;Yantao Liang,&nbsp;Yundan Liu,&nbsp;Xinran Zhang,&nbsp;Wenjing Zhang,&nbsp;Ziyue Wang,&nbsp;Hongbing Shao,&nbsp;Yeong Yik Sung,&nbsp;Wen Jye Mok,&nbsp;Li Lian Wong,&nbsp;Andrew McMinn,&nbsp;Min Wang","doi":"10.1007/s42995-023-00166-1","DOIUrl":"10.1007/s42995-023-00166-1","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1007/s42995-022-00160-z.].</p>","PeriodicalId":53218,"journal":{"name":"Marine Life Science & Technology","volume":"5 2","pages":"286-288"},"PeriodicalIF":5.7,"publicationDate":"2023-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10232385/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9570729","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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