Pub Date : 2024-09-25eCollection Date: 2024-01-01DOI: 10.3389/fmicb.2024.1444235
Bin Yin, Can Mao, Fangzhao Yu, Wangdong Li, Runhong Pan, Wei Feng, Yong Li
In this study, a ddPCR method for the detection of scale drop disease virus (SDDV) in yellowfin seabream (Acanthopagrus latus) was established based on Real-time fluorescence quantitative PCR detection methods and principles. The reaction conditions were optimized, and the sensitivity, specificity, accuracy, and reproducibility were assessed. The results showed that threshold line position was determined to be 1900 by the ddPCR method; the optimum annealing temperature for SDDV detection by the ddPCR method was 60°C; the limit of detection was 1.4-1.7 copies/μL; the results of specific detection of other common viruses, except for SDDV specific amplification, were all negative; and the relative standard deviation (RSD) for the reproducibility validation was 0.77%. The samples of yellowfin seabream (Acanthopagrus latus) liver, spleen, kidney, heart, intestine, brain, blood, muscle, skin and ascites with three replicates, respectively, were tested using the ddPCR method, and the results were consistent with clinical findings. The ddPCR method established in this study has the advantages of high sensitivity, high specificity, good reproducibility and simple steps for the quantitative detection of SDDV, which could be used for the nucleic acid detection of clinical SDDV samples, and provided a new quantitative method for the diagnosis of yellowfin seabream SDDV in the early stage of pathogenesis.
{"title":"A droplet digital PCR method for the detection of scale drop disease virus in yellowfin seabream (<i>Acanthopagrus latus</i>).","authors":"Bin Yin, Can Mao, Fangzhao Yu, Wangdong Li, Runhong Pan, Wei Feng, Yong Li","doi":"10.3389/fmicb.2024.1444235","DOIUrl":"10.3389/fmicb.2024.1444235","url":null,"abstract":"<p><p>In this study, a ddPCR method for the detection of scale drop disease virus (SDDV) in yellowfin seabream (<i>Acanthopagrus latus</i>) was established based on Real-time fluorescence quantitative PCR detection methods and principles. The reaction conditions were optimized, and the sensitivity, specificity, accuracy, and reproducibility were assessed. The results showed that threshold line position was determined to be 1900 by the ddPCR method; the optimum annealing temperature for SDDV detection by the ddPCR method was 60°C; the limit of detection was 1.4-1.7 copies/μL; the results of specific detection of other common viruses, except for SDDV specific amplification, were all negative; and the relative standard deviation (RSD) for the reproducibility validation was 0.77%. The samples of yellowfin seabream (<i>Acanthopagrus latus</i>) liver, spleen, kidney, heart, intestine, brain, blood, muscle, skin and ascites with three replicates, respectively, were tested using the ddPCR method, and the results were consistent with clinical findings. The ddPCR method established in this study has the advantages of high sensitivity, high specificity, good reproducibility and simple steps for the quantitative detection of SDDV, which could be used for the nucleic acid detection of clinical SDDV samples, and provided a new quantitative method for the diagnosis of yellowfin seabream SDDV in the early stage of pathogenesis.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11461249/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142389362","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}
Pub Date : 2024-09-25eCollection Date: 2024-01-01DOI: 10.3389/fmicb.2024.1476087
Zaizhu Yuan, Zhengkai Ge, Qingquan Fu, Fangfang Wang, Qingling Wang, Xuewei Shi, Bin Wang
Introduction: Low temperature inhibits the growth of most microorganisms. However, some microbes can grow well in a low temperature, even a freezing temperature.
Methods: In this study, the mechanisms conferring cold resistance in the cryophylactic yeast Metschnikowia (M.) pulcherrima MS612, an isolate of the epidermis of ice grapes, were investigated based on comparative transcriptome analysis.
Results: A total of 6018 genes and 374 differentially expressed genes (> 2-fold, p < 0.05) were identified using RNA-Seq. The differentially expressed genes were mainly involved in carbohydrate and energy metabolism, transport mechanisms, antifreeze protection, lipid synthesis, and signal transduction. M. pulcherrima MS612 maintained normal growth at low temperature (5°C) by enhancing energy metabolism, sterol synthesis, metal ion homeostasis, amino acid and MDR transport, while increased synthesis of glycerol and proline transport to improve its resistance to the freezing temperature (-5°C). Furthermore, cAMP-PKA and ERAD signaling pathways contribute to resist the low temperature and the freezing temperature, respectively.
Conclusion: This study provides new insights into cold resistance in cryophylactic microorganisms for maneuvering various metabolism to resist different cold environment.
{"title":"Investigation of cold-resistance mechanisms in cryophylactic yeast <i>Metschnikowia pulcherrima</i> based on comparative transcriptome analysis.","authors":"Zaizhu Yuan, Zhengkai Ge, Qingquan Fu, Fangfang Wang, Qingling Wang, Xuewei Shi, Bin Wang","doi":"10.3389/fmicb.2024.1476087","DOIUrl":"10.3389/fmicb.2024.1476087","url":null,"abstract":"<p><strong>Introduction: </strong>Low temperature inhibits the growth of most microorganisms. However, some microbes can grow well in a low temperature, even a freezing temperature.</p><p><strong>Methods: </strong>In this study, the mechanisms conferring cold resistance in the cryophylactic yeast <i>Metschnikowia</i> (<i>M.</i>) <i>pulcherrima</i> MS612, an isolate of the epidermis of ice grapes, were investigated based on comparative transcriptome analysis.</p><p><strong>Results: </strong>A total of 6018 genes and 374 differentially expressed genes (> 2-fold, <i>p</i> < 0.05) were identified using RNA-Seq. The differentially expressed genes were mainly involved in carbohydrate and energy metabolism, transport mechanisms, antifreeze protection, lipid synthesis, and signal transduction. <i>M. pulcherrima</i> MS612 maintained normal growth at low temperature (5°C) by enhancing energy metabolism, sterol synthesis, metal ion homeostasis, amino acid and MDR transport, while increased synthesis of glycerol and proline transport to improve its resistance to the freezing temperature (-5°C). Furthermore, cAMP-PKA and ERAD signaling pathways contribute to resist the low temperature and the freezing temperature, respectively.</p><p><strong>Conclusion: </strong>This study provides new insights into cold resistance in cryophylactic microorganisms for maneuvering various metabolism to resist different cold environment.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11462854/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142389399","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}
Pub Date : 2024-09-24eCollection Date: 2024-01-01DOI: 10.3389/fmicb.2024.1421101
Annica Marie Brink, Anke Kremp, Elena Gorokhova
In the Baltic Sea, the dinoflagellates Apocalathium malmogiense, Biecheleria baltica, and Gymnodinium corollarium are important contributors to the spring bloom. However, their relative contribution to the bloom community cannot be unambiguously determined by conventional light microscopy due to a lack of resolution of distinctive morphological features of the three species. Here, we describe a molecular approach based on a quantitative real-time polymerase chain reaction (qPCR) primer and probe system, targeting the ITS1 and ITS2 regions of the rRNA gene for all three species and enabling their quantification. The specificity of the method was demonstrated using monocultures of A. malmogiense, B. baltica, G. corollarium as well as three other dinoflagellate species co-occurring in the Baltic Sea during spring and validated using field-collected phytoplankton samples.
{"title":"Quantitative real-time PCR assays for species-specific detection and quantification of Baltic Sea spring bloom dinoflagellates.","authors":"Annica Marie Brink, Anke Kremp, Elena Gorokhova","doi":"10.3389/fmicb.2024.1421101","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1421101","url":null,"abstract":"<p><p>In the Baltic Sea, the dinoflagellates <i>Apocalathium malmogiense</i>, <i>Biecheleria baltica</i>, and <i>Gymnodinium corollarium</i> are important contributors to the spring bloom. However, their relative contribution to the bloom community cannot be unambiguously determined by conventional light microscopy due to a lack of resolution of distinctive morphological features of the three species. Here, we describe a molecular approach based on a quantitative real-time polymerase chain reaction (qPCR) primer and probe system, targeting the ITS1 and ITS2 regions of the rRNA gene for all three species and enabling their quantification. The specificity of the method was demonstrated using monocultures of <i>A. malmogiense</i>, <i>B. baltica</i>, <i>G. corollarium</i> as well as three other dinoflagellate species co-occurring in the Baltic Sea during spring and validated using field-collected phytoplankton samples.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11458424/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142389418","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}
Tabanids, commonly known as horseflies and belonging to the family Tabanidae, are blood-feeding arthropods (BFA) found worldwide. They are known for their ability to mechanically and biologically transmit various animal pathogens. Tabanids are potential vectors for diseases such as Francisella tularensis, Anaplasma marginale, Theileria spp., and contributors to lumpy skin diseases. Despite their involvement in common BFA studies, tabanids have not been extensively explored in microbiome research. In this study, the microbiota structure and composition in various organs of four distinct genera of tabanids: Atylotus, Haematopota, Tabanus, and Hybomitra were examined. High-throughput sequencing of the bacterial 16S rRNA gene was performed to gain insights into the microbial communities associated with the different tabanid species. Result display that microbiota composition and diversity, including Firmicutes, Proteobacteria, and Bacteroidetes, varied significantly among the different organs, with the ovaries exhibiting significantly higher diversity. Apart from the Haematopota genus, Tenericutes were enriched in the midgut of other tabanid species, whereas the Malpighian tubules exhibited a higher abundance of Bacteroides. Notably, the ovarian microbiota structure was conserved among the four tabanid species, indicating its potential association with reproductive development. Evaluation of the potential pathogen risk revealed putative pathogens in over 100 genera associated with these tabanid commensal organisms. Twenty genera were annotated as zoonotic agents with a high abundance of Citrobacter and Brucella, highlighting the presence of this important group of zoonotic pathogens. Functional predictions of vector-microbiota interactions indicate that microbiota significantly affects vector biological traits and can influence pathogen transmission via direct interactions or by regulating host immunity and nutrition. For the first time, the distribution characteristics and functions of four genera of horsefly microbiota were analyzed, revealing the presence of multiple potential pathogenic microorganisms. These findings provide valuable insights for future research and the development of symbiotic-based strategies to control insect-borne diseases among tabanids.
{"title":"Microbiota profile in organs of the horseflies (Diptera: Tabanidae) in Northeastern China.","authors":"Hong-Yu Qiu, Qing-Bo Lv, Chun-Ren Wang, Hao Ju, Chun-Feng Luo, Shun-Shuai Liu, Mu-Han Na, Qiao-Cheng Chang, Jia-Fu Jiang","doi":"10.3389/fmicb.2024.1467875","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1467875","url":null,"abstract":"<p><p>Tabanids, commonly known as horseflies and belonging to the family Tabanidae, are blood-feeding arthropods (BFA) found worldwide. They are known for their ability to mechanically and biologically transmit various animal pathogens. Tabanids are potential vectors for diseases such as <i>Francisella tularensis, Anaplasma marginale, Theileria</i> spp., and contributors to lumpy skin diseases. Despite their involvement in common BFA studies, tabanids have not been extensively explored in microbiome research. In this study, the microbiota structure and composition in various organs of four distinct genera of tabanids: <i>Atylotus</i>, <i>Haematopota</i>, <i>Tabanus</i>, and <i>Hybomitra</i> were examined. High-throughput sequencing of the bacterial 16S rRNA gene was performed to gain insights into the microbial communities associated with the different tabanid species. Result display that microbiota composition and diversity, including Firmicutes, Proteobacteria, and Bacteroidetes, varied significantly among the different organs, with the ovaries exhibiting significantly higher diversity. Apart from the <i>Haematopota</i> genus, <i>Tenericutes</i> were enriched in the midgut of other tabanid species, whereas the Malpighian tubules exhibited a higher abundance of Bacteroides. Notably, the ovarian microbiota structure was conserved among the four tabanid species, indicating its potential association with reproductive development. Evaluation of the potential pathogen risk revealed putative pathogens in over 100 genera associated with these tabanid commensal organisms. Twenty genera were annotated as zoonotic agents with a high abundance of <i>Citrobacter</i> and <i>Brucella</i>, highlighting the presence of this important group of zoonotic pathogens. Functional predictions of vector-microbiota interactions indicate that microbiota significantly affects vector biological traits and can influence pathogen transmission via direct interactions or by regulating host immunity and nutrition. For the first time, the distribution characteristics and functions of four genera of horsefly microbiota were analyzed, revealing the presence of multiple potential pathogenic microorganisms. These findings provide valuable insights for future research and the development of symbiotic-based strategies to control insect-borne diseases among tabanids.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11458529/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142389402","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}
Pub Date : 2024-09-24eCollection Date: 2024-01-01DOI: 10.3389/fmicb.2024.1458369
Jayaraman Narenkumar, Bhaskar Das, Subramani Abilaji, Kuppusamy Sathishkumar, Mohamad S AlSalhi, Sandhanasamy Devanesan, Aruliah Rajasekar, Tabarak Malik
Background: Environmental soil contamination is a serious problem for humans worldwide, as it causes many diseases.
Methods: The present study focuses on utilizing biosurfactants produced by Pseudomonas stutzeri (P. stutzeri) NA3 and Bacillus cereus (B. cereus) EN6, as an electrolyte for removing chromium (Cr) from contaminated soil using the electrokinetic (EK) process.
Results: As a result, biosurfactants produced by P. stutzeri NA3 and B. cereus EN6, being lipopeptides, increase heavy metal mobility in the EK process. The Cr removal efficiency of a novel electrolyte (biosurfactants) in the EK process was compared with that of NA3 and EN6 biosurfactants. The EK results revealed a maximum Cr removal of 75 and 70% by NA3 and EN6, respectively, at the end of 7 days.
Discussion: The biosurfactant aids in the breaking down of the heavy metals that are present deeper into the soil matrix. From the metagenomics analysis, it was identified that biosurfactant changes the microbial community with an enhanced ability to remove heavy metals. The phytotoxicity assay confirms that NA3 biosurfactant solution showed 95% seed germination and can lower hazardous pollutants in the soil.
Conclusion: The application of biosurfactants as a potent electrolyte for the remediation of hazardous pollutants is an integrated process. Overall, the results of this study suggest that biosurfactants can serve as an economic and efficient electrolyte in the EK process to remove Cr from polluted soil.
背景环境土壤污染是全世界人类面临的一个严重问题,因为它会导致许多疾病:本研究的重点是利用施特泽假单胞菌(P. stutzeri)NA3和蜡样芽孢杆菌(B. cereus)EN6产生的生物表面活性剂作为电解质,采用电动(EK)工艺去除污染土壤中的铬(Cr):结果:由 P. stutzeri NA3 和 B. cereus EN6 产生的生物表面活性剂(脂肽)在 EK 过程中增加了重金属的流动性。比较了新型电解质(生物表面活性剂)与 NA3 和 EN6 生物表面活性剂在 EK 过程中的铬去除效率。EK 结果显示,在 7 天结束时,NA3 和 EN6 对铬的最大去除率分别为 75% 和 70%:讨论:生物表面活性剂有助于分解存在于土壤基质深层的重金属。元基因组学分析表明,生物表面活性剂改变了微生物群落,增强了清除重金属的能力。植物毒性试验证实,NA3 生物表面活性剂溶液的种子发芽率为 95%,可降低土壤中的有害污染物:将生物表面活性剂作为一种有效的电解质用于有害污染物的修复是一个综合过程。总之,本研究的结果表明,生物表面活性剂可作为 EK 过程中一种经济、高效的电解质,用于去除污染土壤中的铬。
{"title":"Biosurfactant-assisted bio-electrokinetic enhanced remediation of heavy metal-contaminated soil.","authors":"Jayaraman Narenkumar, Bhaskar Das, Subramani Abilaji, Kuppusamy Sathishkumar, Mohamad S AlSalhi, Sandhanasamy Devanesan, Aruliah Rajasekar, Tabarak Malik","doi":"10.3389/fmicb.2024.1458369","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1458369","url":null,"abstract":"<p><strong>Background: </strong>Environmental soil contamination is a serious problem for humans worldwide, as it causes many diseases.</p><p><strong>Methods: </strong>The present study focuses on utilizing biosurfactants produced by <i>Pseudomonas stutzeri</i> (<i>P. stutzeri</i>) NA3 and <i>Bacillus cereus</i> (<i>B. cereus</i>) EN6, as an electrolyte for removing chromium (Cr) from contaminated soil using the electrokinetic (EK) process.</p><p><strong>Results: </strong>As a result, biosurfactants produced by <i>P. stutzeri</i> NA3 and <i>B. cereus</i> EN6, being lipopeptides, increase heavy metal mobility in the EK process. The Cr removal efficiency of a novel electrolyte (biosurfactants) in the EK process was compared with that of NA3 and EN6 biosurfactants. The EK results revealed a maximum Cr removal of 75 and 70% by NA3 and EN6, respectively, at the end of 7 days.</p><p><strong>Discussion: </strong>The biosurfactant aids in the breaking down of the heavy metals that are present deeper into the soil matrix. From the metagenomics analysis, it was identified that biosurfactant changes the microbial community with an enhanced ability to remove heavy metals. The phytotoxicity assay confirms that NA3 biosurfactant solution showed 95% seed germination and can lower hazardous pollutants in the soil.</p><p><strong>Conclusion: </strong>The application of biosurfactants as a potent electrolyte for the remediation of hazardous pollutants is an integrated process. Overall, the results of this study suggest that biosurfactants can serve as an economic and efficient electrolyte in the EK process to remove Cr from polluted soil.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11458532/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142389381","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}
Prokaryotes play a crucial role in marine ecosystem health and drive biogeochemical processes. The northern Ninety East Ridge (NER) of the Indian Ocean, a pivotal yet understudied area for these cycles, has been the focus of our study. We employed high-throughput 16S rRNA gene sequencing to analyze 35 water samples from five stations along the ridge, categorized into three depth- and dissolved oxygen-level-based groups. Our approach uncovered a clear stratification of microbial communities, with key bioindicators such as Prochlorococcus MIT9313, Sva0996 marine group, and Candidatus Actinomarina in the upper layer; Ketobacter, Pseudophaeobacter, Nitrospina, and SAR324 clade in the middle layer; and Methylobacterium-Methylorubrum, Sphingomonas, Sphingobium, and Erythrobacter in the deep layer. Methylobacterium-Methylorubrum emerged as the most abundant bacterial genus, while Nitrosopumilaceae predominated among archaeal communities. The spatial and depth-wise distribution patterns revealed that Ketobacter was unique to the northern NER, whereas Methylobacterium-Methylorubrum, UBA10353, SAR324 clade, SAR406, Sva0996_marine_group, Candidatus Actinomarina were ubiquitous across various marine regions, exhibiting niche differentiation at the OTU level. Environmental factors, especially dissolved oxygen (DO), silicate, nitrate, and salinity, significantly influence community structure. These findings not only reveal the novelty and adaptability of the microbial ecosystem in the northern NER but also contribute to the broader understanding of marine microbial diversity and its response to environmental heterogeneity.
原核生物在海洋生态系统健康和生物地球化学过程中发挥着至关重要的作用。印度洋九十东海脊(NER)北部是这些循环的关键区域,但研究不足,因此成为我们研究的重点。我们采用高通量 16S rRNA 基因测序技术,分析了来自海脊沿线五个站点的 35 份水样,并根据深度和溶解氧水平分为三组。我们的方法揭示了微生物群落的明显分层,上层的关键生物指标包括原绿球菌 MIT9313、Sva0996 海洋组和放线菌;中层的酮细菌、假杆菌、硝化细菌和 SAR324 支系;深层的甲基弯曲杆菌-甲基瘤菌、鞘氨单胞菌、鞘氨梭菌和红球菌。在古细菌群落中,甲基弯曲杆菌(Methylobacterium-Methylorubrum)是数量最多的细菌属,而硝基古细菌(Nitrosopumilaceae)则占主导地位。从空间和深度分布模式来看,Ketobacter 为北部 NER 所独有,而 Methylobacterium-Methylorubrum、UBA10353、SAR324 支系、SAR406、Sva0996_marine_group、Candidatus Actinomarina 则在各海洋区域无处不在,表现出 OTU 水平的生态位分化。环境因素,尤其是溶解氧(DO)、硅酸盐、硝酸盐和盐度对群落结构有显著影响。这些发现不仅揭示了北部近海区域微生物生态系统的新颖性和适应性,而且有助于更广泛地了解海洋微生物多样性及其对环境异质性的响应。
{"title":"Unveiling the microbial diversity across the northern Ninety East Ridge in the Indian Ocean.","authors":"Ding Li, Liping Wang, Fan Jiang, Xiang Zeng, Qinzeng Xu, Xuelei Zhang, Qiang Zheng, Zongze Shao","doi":"10.3389/fmicb.2024.1436735","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1436735","url":null,"abstract":"<p><p>Prokaryotes play a crucial role in marine ecosystem health and drive biogeochemical processes. The northern Ninety East Ridge (NER) of the Indian Ocean, a pivotal yet understudied area for these cycles, has been the focus of our study. We employed high-throughput 16S rRNA gene sequencing to analyze 35 water samples from five stations along the ridge, categorized into three depth- and dissolved oxygen-level-based groups. Our approach uncovered a clear stratification of microbial communities, with key bioindicators such as <i>Prochlorococcus</i> MIT9313, Sva0996 marine group, and <i>Candidatus Actinomarina</i> in the upper layer; <i>Ketobacter</i>, <i>Pseudophaeobacter</i>, <i>Nitrospina</i>, and SAR324 clade in the middle layer; and <i>Methylobacterium-Methylorubrum</i>, <i>Sphingomonas</i>, <i>Sphingobium</i>, and <i>Erythrobacter</i> in the deep layer. <i>Methylobacterium-Methylorubrum</i> emerged as the most abundant bacterial genus, while <i>Nitrosopumilaceae</i> predominated among archaeal communities. The spatial and depth-wise distribution patterns revealed that <i>Ketobacter</i> was unique to the northern NER, whereas <i>Methylobacterium-Methylorubrum</i>, UBA10353, SAR324 clade, SAR406, Sva0996_marine_group, <i>Candidatus Actinomarina</i> were ubiquitous across various marine regions, exhibiting niche differentiation at the OTU level. Environmental factors, especially dissolved oxygen (DO), silicate, nitrate, and salinity, significantly influence community structure. These findings not only reveal the novelty and adaptability of the microbial ecosystem in the northern NER but also contribute to the broader understanding of marine microbial diversity and its response to environmental heterogeneity.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11458393/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142389422","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}
Pub Date : 2024-09-24eCollection Date: 2024-01-01DOI: 10.3389/fmicb.2024.1392808
Adolfo Isla, Marcelo Aguilar, Sandra N Flores-Martin, Claudia A Barrientos, Genaro Soto-Rauch, Jorge Mancilla-Schulz, Felipe Almendras, Jaime Figueroa, Alejandro J Yañez
Introduction: Piscirickettsia salmonis, the causative agent of Piscirickettsiosis, poses a significant threat to the Chilean aquaculture industry, resulting in substantial economic losses annually. The pathogen, first identified as specie in 1992, this pathogen was divided into two genogroups: LF-89 and EM-90, associated with different phenotypic mortality and pathogenicity. Traditional genotyping methods, such as multiplex PCR, are effective but limited by their cost, equipment requirements, and the need for specialized expertise.
Methods: This study validates Loop-mediated Isothermal Amplification (LAMP) as a rapid and specific alternative for diagnosing P. salmonis infections. We developed the first qPCR and LAMP assay targeting the species-conserved tonB receptor gene (tonB-r, WP_016210144.1) for the specific species-level identification of P. salmonis. Additionally, we designed two genotyping LAMP assays to differentiate between the LF-89 and EM-90 genogroups, utilizing the unique coding sequences Nitronate monooxygenase (WP_144420689.1) for LF-89 and Acid phosphatase (WP_016210154.1) for EM-90.
Results: The LAMP assays demonstrated sensitivity and specificity comparable to real-time PCR, with additional benefits including rapid results, lower costs, and simplified operation, making them particularly suitable for field use. Specificity was confirmed by testing against other salmonid pathogens, such as Renibacterium salmoninarum, Vibrio ordalii, Flavobacterium psychrophilum, Tenacibaculum maritimum, and Aeromonas salmonicida, with no cross-reactivity observed.
Discussion: The visual detection method and precise differentiation between genogroups underscore LAMP's potential as a robust diagnostic tool for aquaculture. This advancement in the specie detection (qPCR and LAMP) and genotyping of P. salmonis represents a significant step forward in disease management within the aquaculture industry. The implementation of LAMP promises enhanced disease surveillance, early detection, and improved management strategies, ultimately benefiting the salmonid aquaculture sector.
{"title":"Advancements in rapid diagnostics and genotyping of <i>Piscirickettsia salmonis</i> using Loop-mediated Isothermal Amplification.","authors":"Adolfo Isla, Marcelo Aguilar, Sandra N Flores-Martin, Claudia A Barrientos, Genaro Soto-Rauch, Jorge Mancilla-Schulz, Felipe Almendras, Jaime Figueroa, Alejandro J Yañez","doi":"10.3389/fmicb.2024.1392808","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1392808","url":null,"abstract":"<p><strong>Introduction: </strong><i>Piscirickettsia salmonis</i>, the causative agent of Piscirickettsiosis, poses a significant threat to the Chilean aquaculture industry, resulting in substantial economic losses annually. The pathogen, first identified as specie in 1992, this pathogen was divided into two genogroups: LF-89 and EM-90, associated with different phenotypic mortality and pathogenicity. Traditional genotyping methods, such as multiplex PCR, are effective but limited by their cost, equipment requirements, and the need for specialized expertise.</p><p><strong>Methods: </strong>This study validates Loop-mediated Isothermal Amplification (LAMP) as a rapid and specific alternative for diagnosing P. salmonis infections. We developed the first qPCR and LAMP assay targeting the species-conserved tonB receptor gene (<i>ton</i>B-r, WP_016210144.1) for the specific species-level identification of <i>P. salmonis</i>. Additionally, we designed two genotyping LAMP assays to differentiate between the LF-89 and EM-90 genogroups, utilizing the unique coding sequences Nitronate monooxygenase (WP_144420689.1) for LF-89 and Acid phosphatase (WP_016210154.1) for EM-90.</p><p><strong>Results: </strong>The LAMP assays demonstrated sensitivity and specificity comparable to real-time PCR, with additional benefits including rapid results, lower costs, and simplified operation, making them particularly suitable for field use. Specificity was confirmed by testing against other salmonid pathogens, such as <i>Renibacterium salmoninarum, Vibrio ordalii, Flavobacterium psychrophilum, Tenacibaculum maritimum</i>, and <i>Aeromonas salmonicida</i>, with no cross-reactivity observed.</p><p><strong>Discussion: </strong>The visual detection method and precise differentiation between genogroups underscore LAMP's potential as a robust diagnostic tool for aquaculture. This advancement in the specie detection (qPCR and LAMP) and genotyping of <i>P. salmonis</i> represents a significant step forward in disease management within the aquaculture industry. The implementation of LAMP promises enhanced disease surveillance, early detection, and improved management strategies, ultimately benefiting the salmonid aquaculture sector.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11458457/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142389363","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}
Pub Date : 2024-09-24eCollection Date: 2024-01-01DOI: 10.3389/fmicb.2024.1455462
Jason C Hsu, Panatda Saenkham-Huntsinger, Pinghan Huang, Cassio Pontes Octaviani, Aleksandra K Drelich, Bi-Hung Peng, Chien-Te K Tseng
COVID-19 presents with a plethora of neurological signs and symptoms despite being characterized as a respiratory disease, including seizures, anxiety, depression, amnesia, attention deficits, and alterations in consciousness. The olfactory nerve is widely accepted as the neuroinvasive route by which the etiological agent SARS-CoV-2 enters the brain, but the trigeminal nerve is an often-overlooked additional route. Based on this consensus, we initially conducted a pilot experiment investigating the olfactory nerve route of SARS-CoV-2 neuroinvasion via intranasal inoculation in AC70 human ACE2 transgenic mice. Notably, we found that the trigeminal ganglion is an early and highly efficient site of viral replication, which then rapidly spread widely throughout the brain where neurons were primarily targeted. Despite the extensive viral infection across the brain, obvious evidence of tissue pathology including inflammatory infiltration, glial activation, and apoptotic cell deaths were not consistently observed, albeit inflammatory cytokines were significantly induced. However, the expression levels of different genes related to neuronal function, including the neurotransmitter dopamine pathway as well as synaptic function, and markers of neuronal damage were altered as compared to mock-infected mice. Our findings suggest that the trigeminal nerve may serve as a neuroinvasive route complementary to the olfactory nerve and that the ensuing neuroinvasion presented a unique neuropathological profile. This study provides insights into potential neuropathogenic mechanisms utilized by coronaviruses.
{"title":"Characterizing neuroinvasion and neuropathology of SARS-CoV-2 by using AC70 human ACE2 transgenic mice.","authors":"Jason C Hsu, Panatda Saenkham-Huntsinger, Pinghan Huang, Cassio Pontes Octaviani, Aleksandra K Drelich, Bi-Hung Peng, Chien-Te K Tseng","doi":"10.3389/fmicb.2024.1455462","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1455462","url":null,"abstract":"<p><p>COVID-19 presents with a plethora of neurological signs and symptoms despite being characterized as a respiratory disease, including seizures, anxiety, depression, amnesia, attention deficits, and alterations in consciousness. The olfactory nerve is widely accepted as the neuroinvasive route by which the etiological agent SARS-CoV-2 enters the brain, but the trigeminal nerve is an often-overlooked additional route. Based on this consensus, we initially conducted a pilot experiment investigating the olfactory nerve route of SARS-CoV-2 neuroinvasion via intranasal inoculation in AC70 human ACE2 transgenic mice. Notably, we found that the trigeminal ganglion is an early and highly efficient site of viral replication, which then rapidly spread widely throughout the brain where neurons were primarily targeted. Despite the extensive viral infection across the brain, obvious evidence of tissue pathology including inflammatory infiltration, glial activation, and apoptotic cell deaths were not consistently observed, albeit inflammatory cytokines were significantly induced. However, the expression levels of different genes related to neuronal function, including the neurotransmitter dopamine pathway as well as synaptic function, and markers of neuronal damage were altered as compared to mock-infected mice. Our findings suggest that the trigeminal nerve may serve as a neuroinvasive route complementary to the olfactory nerve and that the ensuing neuroinvasion presented a unique neuropathological profile. This study provides insights into potential neuropathogenic mechanisms utilized by coronaviruses.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11458418/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142389382","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}
Pub Date : 2024-09-24eCollection Date: 2024-01-01DOI: 10.3389/fmicb.2024.1464719
Chang Liu, Chenxuan Cui, Xiaoxin Tan, Junjie Miao, Wei Wang, Han Ren, Hua Wu, Cuiying Zheng, Huan Ren, Weijun Kang
The emergence of multidrug-resistant Pseudomonas aeruginosa isolates is a growing concern for public health, necessitating new therapeutic strategies. Gallium nitrate [Ga(NO3)3], a medication for cancer-related hypercalcemia, has attracted great attention due to its ability to inhibit P. aeruginosa growth and biofilm formation by disrupting iron metabolism. However, the antibacterial efficacy of Ga(NO3)3 is not always satisfactory. It is imperative to investigate the factors that affect the bactericidal effects of Ga(NO3)3 and to identify new ways to enhance its efficacy. This study focused on the impact of pH on P. aeruginosa resistance to Ga(NO3)3, along with the underlying mechanism. The results indicate that acidic conditions could increase the effectiveness of Ga(NO3)3 against P. aeruginosa by promoting the production of pyochelin and gallium uptake. Subsequently, using glutamic acid, a clinically compatible acidic amino acid, the pH was significantly lowered and enhanced the bactericidal and inhibitory efficacy of Ga(NO3)3 against biofilm formation by P. aeruginosa, including a reference strain PA14 and several multidrug-resistant clinical isolates. Furthermore, we used an abscess mouse model to evaluate this combination in vivo; the results show that the combination of glutamic acid and Ga(NO3)3 significantly improved P. aeruginosa clearance. Overall, the present study demonstrates that acidic conditions can increase the sensitivity of P. aeruginosa to Ga(NO3)3. Combining glutamic acid and Ga(NO3)3 is a potential strategy for the treatment of P. aeruginosa infections.
{"title":"pH-mediated potentiation of gallium nitrate against <i>Pseudomonas aeruginosa</i>.","authors":"Chang Liu, Chenxuan Cui, Xiaoxin Tan, Junjie Miao, Wei Wang, Han Ren, Hua Wu, Cuiying Zheng, Huan Ren, Weijun Kang","doi":"10.3389/fmicb.2024.1464719","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1464719","url":null,"abstract":"<p><p>The emergence of multidrug-resistant <i>Pseudomonas aeruginosa</i> isolates is a growing concern for public health, necessitating new therapeutic strategies. Gallium nitrate [Ga(NO<sub>3</sub>)<sub>3</sub>], a medication for cancer-related hypercalcemia, has attracted great attention due to its ability to inhibit <i>P. aeruginosa</i> growth and biofilm formation by disrupting iron metabolism. However, the antibacterial efficacy of Ga(NO<sub>3</sub>)<sub>3</sub> is not always satisfactory. It is imperative to investigate the factors that affect the bactericidal effects of Ga(NO<sub>3</sub>)<sub>3</sub> and to identify new ways to enhance its efficacy. This study focused on the impact of pH on <i>P. aeruginosa</i> resistance to Ga(NO<sub>3</sub>)<sub>3</sub>, along with the underlying mechanism. The results indicate that acidic conditions could increase the effectiveness of Ga(NO<sub>3</sub>)<sub>3</sub> against <i>P. aeruginosa</i> by promoting the production of pyochelin and gallium uptake. Subsequently, using glutamic acid, a clinically compatible acidic amino acid, the pH was significantly lowered and enhanced the bactericidal and inhibitory efficacy of Ga(NO<sub>3</sub>)<sub>3</sub> against biofilm formation by <i>P. aeruginosa</i>, including a reference strain PA14 and several multidrug-resistant clinical isolates. Furthermore, we used an abscess mouse model to evaluate this combination <i>in vivo</i>; the results show that the combination of glutamic acid and Ga(NO<sub>3</sub>)<sub>3</sub> significantly improved <i>P. aeruginosa</i> clearance. Overall, the present study demonstrates that acidic conditions can increase the sensitivity of <i>P. aeruginosa</i> to Ga(NO<sub>3</sub>)<sub>3</sub>. Combining glutamic acid and Ga(NO<sub>3</sub>)<sub>3</sub> is a potential strategy for the treatment of <i>P. aeruginosa</i> infections.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11458400/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142389416","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}
ASFV C315R is homologous to the transcription factor TFIIB of large unclassified DNA viruses, and H359L is identical to the subunit 3 (RPB3) of eukaryotic RNA polymerase II. The C315R and H359L may play an important role in ASFV replication and transcription. Here, we evaluated the biological function of the C315R and H359L genes during virus replication in vitro and during infection in pigs. Results showed that C315R and H359L are highly conserved among ASFV genotype II strains; quantitative PCR (qPCR) and western blotting analyses revealed that C315R and H359L are early transcribed genes prior to viral DNA replication, but their protein expression is delayed. The immunofluorescence and western blotting analysis revealed that both proteins localized in the cell cytoplasm and nucleus at 24 h post infection, however, pH359L was mainly detected in the cell cytoplasm. Furthermore, overexpression of pH359L in MA104 cells significantly increased viral titer, RNA transcription levels, and viral protein expression levels, while overexpression of pC315R slightly enhanced ASFV replication. In contrast, siRNA targeting ASFV-H359L or C315R reduced replication efficiency in porcine macrophage culture compared to the parent ASFV-CN/SC/2019, demonstrating that C315R and H359L genes are necessary for ASFV replication. Finally, the functional role of C315R or H359L on PKR and eIF2α phosphorylation status and SG formation, as well as cytokine production were evaluated. These studies demonstrated that C315R and H359L are involved in virus replication processes in swine and play important roles in ASFV replication.
{"title":"African swine fever virus RNA polymerase subunits C315R and H359L inhibition host translation by activating the PKR-eIF2a pathway and suppression inflammatory responses.","authors":"Saixia Yang, Yiwang Wang, Jifei Yang, Zhancheng Tian, Mengli Wu, Hualin Sun, Xiaoqiang Zhang, Yaru Zhao, Jianxun Luo, Guiquan Guan, Hong Yin, Rongzeng Hao, Qingli Niu","doi":"10.3389/fmicb.2024.1469166","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1469166","url":null,"abstract":"<p><p>ASFV C315R is homologous to the transcription factor TFIIB of large unclassified DNA viruses, and H359L is identical to the subunit 3 (RPB3) of eukaryotic RNA polymerase II. The C315R and H359L may play an important role in ASFV replication and transcription. Here, we evaluated the biological function of the <i>C315R</i> and <i>H359L</i> genes during virus replication <i>in vitro</i> and during infection in pigs. Results showed that C315R and H359L are highly conserved among ASFV genotype II strains; quantitative PCR (qPCR) and western blotting analyses revealed that <i>C315R</i> and <i>H359L</i> are early transcribed genes prior to viral DNA replication, but their protein expression is delayed. The immunofluorescence and western blotting analysis revealed that both proteins localized in the cell cytoplasm and nucleus at 24 h post infection, however, pH359L was mainly detected in the cell cytoplasm. Furthermore, overexpression of pH359L in MA104 cells significantly increased viral titer, RNA transcription levels, and viral protein expression levels, while overexpression of pC315R slightly enhanced ASFV replication. In contrast, siRNA targeting ASFV-H359L or C315R reduced replication efficiency in porcine macrophage culture compared to the parent ASFV-CN/SC/2019, demonstrating that <i>C315R</i> and <i>H359L</i> genes are necessary for ASFV replication. Finally, the functional role of C315R or H359L on PKR and eIF2α phosphorylation status and SG formation, as well as cytokine production were evaluated. These studies demonstrated that C315R and H359L are involved in virus replication processes in swine and play important roles in ASFV replication.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11458487/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142389364","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}