Fems Microbiology Letters最新文献_第9页

Variation in growth rates between cultures hinders the cultivation of ammonia-oxidizing bacteria. 培养物之间的生长率差异阻碍了氨氧化细菌的培养。

IF 2.1 4区生物学

Fems Microbiology Letters Pub Date : 2024-01-09 DOI: 10.1093/femsle/fnae013

Rino Isshiki, Hirotsugu Fujitani, Satoshi Tsuneda

引用次数: 0

Correction to: Microbiomes in an acidic rock-water cave system. 更正：酸性岩水洞穴系统中的微生物群。

IF 2.1 4区生物学

Fems Microbiology Letters Pub Date : 2024-01-09 DOI: 10.1093/femsle/fnae017

引用次数: 0

Leveraging aquatic-terrestrial interfaces to capture putative habitat generalists. 利用水生-陆生界面捕捉假定的生境综合体。

IF 2.1 4区生物学

Fems Microbiology Letters Pub Date : 2024-01-09 DOI: 10.1093/femsle/fnae025

Sarah C Richards, William L King, Jeremy L Sutherland, Terrence H Bell

{"title":"Leveraging aquatic-terrestrial interfaces to capture putative habitat generalists.","authors":"Sarah C Richards, William L King, Jeremy L Sutherland, Terrence H Bell","doi":"10.1093/femsle/fnae025","DOIUrl":"10.1093/femsle/fnae025","url":null,"abstract":"Habitat type is a strong determinant of microbial composition. Habitat interfaces, such as the boundary between aquatic and terrestrial systems, present unique combinations of abiotic factors for microorganisms to contend with. Aside from the spillover of certain harmful microorganisms from agricultural soils into water (e.g. fecal coliform bacteria), we know little about the extent of soil-water habitat switching across microbial taxa. In this study, we developed a proof-of-concept system to facilitate the capture of putatively generalist microorganisms that can colonize and persist in both soil and river water. We aimed to examine the phylogenetic breadth of putative habitat switchers and how this varies across different source environments. Microbial composition was primarily driven by recipient environment type, with the strongest phylogenetic signal seen at the order level for river water colonizers. We also identified more microorganisms colonizing river water when soil was collected from a habitat interface (i.e. soil at the side of an intermittently flooded river, compared to soil collected further from water sources), suggesting that environmental interfaces could be important reservoirs of microbial habitat generalists. Continued development of experimental systems that actively capture microorganisms that thrive in divergent habitats could serve as a powerful tool for identifying and assessing the ecological distribution of microbial generalists.","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140326515","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

A universal and constant rate of gene content change traces pangenome flux to LUCA. 基因含量变化的普遍性和恒定性追踪了泛基因组到 LUCA 的变化。

IF 2.2 4区生物学

Fems Microbiology Letters Pub Date : 2024-01-09 DOI: 10.1093/femsle/fnae068

Katharina Trost, Michael R Knopp, Jessica L E Wimmer, Fernando D K Tria, William F Martin

{"title":"A universal and constant rate of gene content change traces pangenome flux to LUCA.","authors":"Katharina Trost, Michael R Knopp, Jessica L E Wimmer, Fernando D K Tria, William F Martin","doi":"10.1093/femsle/fnae068","DOIUrl":"10.1093/femsle/fnae068","url":null,"abstract":"Prokaryotic genomes constantly undergo gene flux via lateral gene transfer, generating a pangenome structure consisting of a conserved core genome surrounded by a more variable accessory genome shell. Over time, flux generates change in genome content. Here, we measure and compare the rate of genome flux for 5655 prokaryotic genomes as a function of amino acid sequence divergence in 36 universally distributed proteins of the informational core (IC). We find a clock of gene content change. The long-term average rate of gene content flux is remarkably constant across all higher prokaryotic taxa sampled, whereby the size of the accessory genome-the proportion of the genome harboring gene content difference for genome pairs-varies across taxa. The proportion of species-level accessory genes per genome, varies from 0% (Chlamydia) to 30%-33% (Alphaproteobacteria, Gammaproteobacteria, and Clostridia). A clock-like rate of gene content change across all prokaryotic taxa sampled suggest that pangenome structure is a general feature of prokaryotic genomes and that it has been in existence since the divergence of bacteria and archaea.","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11394098/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142008539","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Xanthomonas protegens sp. nov., a novel rice seed-associated bacterium, provides in vivo protection against X. oryzae pv. oryzae, the bacterial leaf blight pathogen. 一种新型水稻种子相关细菌黄单胞菌（Xanthomonas protegens sp.

IF 2.2 4区生物学

Fems Microbiology Letters Pub Date : 2024-01-09 DOI: 10.1093/femsle/fnae093

Rekha Rana, Anushika Sharma, Vishnu Narayanan Madhavan, Suresh Korpole, Ramesh V Sonti, Hitendra K Patel, Prabhu B Patil

{"title":"Xanthomonas protegens sp. nov., a novel rice seed-associated bacterium, provides in vivo protection against X. oryzae pv. oryzae, the bacterial leaf blight pathogen.","authors":"Rekha Rana, Anushika Sharma, Vishnu Narayanan Madhavan, Suresh Korpole, Ramesh V Sonti, Hitendra K Patel, Prabhu B Patil","doi":"10.1093/femsle/fnae093","DOIUrl":"10.1093/femsle/fnae093","url":null,"abstract":"Historically, Xanthomonas species are primarily known for their pathogenicity against plants, but recently, there have been more findings of non-pathogenic xanthomonads. In the present study, we report isolates from healthy rice seeds that belong to a new species, Xanthomonas protegens, a protector of the rice plants against a serious pathogenic counterpart, i.e. X. oryzae pv. oryzae upon leaf clip co-inoculation. The new member species is non-pathogenic to rice and lacks a type III secretion system. The pangenome investigation revealed a large number of unique genes, including a novel lipopolysaccharide biosynthetic gene cluster, that might be important in its adaptation. The phylo-taxonogenomic analysis revealed that X. protegens is a taxonomic outlier species of X. sontii, a core, vertically transmitted rice seed endophyte with numerous probiotic properties. Interestingly, X. sontii is also reported as a keystone species of healthy rice seed microbiome. The findings and resources will help in the development of unique gene markers and evolutionary studies of X. sontii as a successful symbiont and X. oryzae as a serious pathogen. Here, we propose X. protegens sp. nov. as a novel species of the genus Xanthomonas with PPL118 = MTCC 13396 = CFBP 9164 = ICMP 25181 as the type strain. PPL117, PPL124, PPL125, and PPL126 are other strains of the species.","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142581476","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Disruption of the pkac2 gene in Pleurotus ostreatus alters cell wall structures and enables mycelial dispersion in liquid culture. Pkac2 基因在 Pleurotus ostreatus 中的破坏改变了细胞壁结构，并使菌丝在液体培养物中分散。

IF 2.2 4区生物学

Fems Microbiology Letters Pub Date : 2024-01-09 DOI: 10.1093/femsle/fnae101

Yuitsu Otsuka, Moriyuki Kawauchi, Kai Yoshizawa, Saori Endo, Kim Schiphof, Kenya Tsuji, Akira Yoshimi, Chihiro Tanaka, Shigekazu Yano, Vladimir Elisashvili, Takehito Nakazawa, Toshikazu Irie, Yoichi Honda

{"title":"Disruption of the pkac2 gene in Pleurotus ostreatus alters cell wall structures and enables mycelial dispersion in liquid culture.","authors":"Yuitsu Otsuka, Moriyuki Kawauchi, Kai Yoshizawa, Saori Endo, Kim Schiphof, Kenya Tsuji, Akira Yoshimi, Chihiro Tanaka, Shigekazu Yano, Vladimir Elisashvili, Takehito Nakazawa, Toshikazu Irie, Yoichi Honda","doi":"10.1093/femsle/fnae101","DOIUrl":"10.1093/femsle/fnae101","url":null,"abstract":"In this study, we developed a mycelial dispersion strain by disrupting the pkac2 gene in the white-rot fungus Pleurotus ostreatus. pkac2 is a catalytic subunit gene of protein kinase A, which regulates several transcription factors related to cell wall synthesis. Liquid cultures of the Δpkac2 strains showed very high mycelial dispersibility and were visibly different from the wild-type (WT) strain. Although growth on agar medium was slower than that of WT, Δpkac2 strains grew faster in liquid culture and had approximately twice the mycelial dry weight of WT after 5 days of culture. Microscopic observations showed that the cell walls of the Δpkac2 strains were thinner compared to WT. The β-glucan content in the cell walls decreased in the pkac2 disruptants, although the transcription levels of β-glucan synthase genes increased. Furthermore, the Δpkac2 strains showed decreased hydrophobicity and stress tolerance compared to WT. These results indicate that disruption of the pkac2 gene in P. ostreatus alters the structure of the cell wall surface layer, resulting in high-density cultures due to mycelial dispersion.","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142681025","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Improved treatment of coking wastewater and higher biodiversity through immobilization of Comamonas sp. ZF-3 supplemented microbial community. 通过固定 Comamonas sp. ZF-3 补充微生物群落，改善焦化废水处理并提高生物多样性。

IF 2.2 4区生物学

Fems Microbiology Letters Pub Date : 2024-01-09 DOI: 10.1093/femsle/fnae095

Ke Yuan, Yanbiao Ma, Qiuyu Li

{"title":"Improved treatment of coking wastewater and higher biodiversity through immobilization of Comamonas sp. ZF-3 supplemented microbial community.","authors":"Ke Yuan, Yanbiao Ma, Qiuyu Li","doi":"10.1093/femsle/fnae095","DOIUrl":"10.1093/femsle/fnae095","url":null,"abstract":"The aim of this study was to investigate the relationship among pollutant removal performance, microbial community structure, and potential gene function of immobilized microorganisms in coking wastewater (CWW) treatment process. The results showed that the immobilized biomass containing strain Comamonas sp. ZF-3 displayed greater resistance to CWW and higher COD, NH4+-N removal efficiency (92%, 60%) than free cells (48%, 7%), meanwhile, the results from GC-MS proved main organic pollutants in CWW including phenolic compounds, heterocyclic compounds, and polycyclic aromatic hydrocarbons were basically removed by immobilized microorganisms. During 123 days of degradation experiment, high-throughput 16S rRNA gene sequencing analysis of immobilized carriers showed more stable and diverse microbial community, which was consistent with simultaneous removal of COD and NH4+-N observed in carrier experiment. Among them, Comamonas sp. ZF-3 continuously remained at the highest proportion (23.25%) in immobilized carrier, while Nitrosomonas (1.47%) and Nitrospira (1.90%) were simultaneously detected. Moreover, microbial community of immobilized carriers showed higher relative abundance of potential function in membrane transport and xenobiotics biodegradation and metabolism, which may indirectly displayed biodegradation activity of immobilized functional microorganisms. This work illustrated the survival status and potential gene function of immobilized microorganisms, and provided basis for practical application of immobilized carriers in CWW treatment.","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142617150","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Characterization of Aeromonas salmonicida mesophilic isolates from Alberta (Canada) allows the development of a more sensitive Dictyostelium discoideum predation test. 对加拿大阿尔伯塔省的嗜中性沙门氏菌分离物进行鉴定，从而开发出一种更灵敏的盘状竹荪捕食试验。

IF 2.2 4区生物学

Fems Microbiology Letters Pub Date : 2024-01-09 DOI: 10.1093/femsle/fnae078

Rébecca E St-Laurent, Antony T Vincent, Valérie E Paquet, Gabrielle R Leduc, Natalia Lorenc, Jennifer Ronholm, Xiaoji Liu, Steve J Charette

{"title":"Characterization of Aeromonas salmonicida mesophilic isolates from Alberta (Canada) allows the development of a more sensitive Dictyostelium discoideum predation test.","authors":"Rébecca E St-Laurent, Antony T Vincent, Valérie E Paquet, Gabrielle R Leduc, Natalia Lorenc, Jennifer Ronholm, Xiaoji Liu, Steve J Charette","doi":"10.1093/femsle/fnae078","DOIUrl":"10.1093/femsle/fnae078","url":null,"abstract":"Aeromonas salmonicida is studied using Dictyostelium discoideum as a model host, with predation resistance measured as a key parameter. Aeromonas salmonicida mesophilic isolates exhibit inconclusive results with the amoebic model. This study focuses on new mesophilic isolates (S24-S38, S26-S10, and S28-S20) from Alberta, Canada, and introduces an improved predation test method. Phylogenetic analysis reveals two subgroups, with S24-S38 and S26-S10 clustering with the subspecies pectinolytica from Argentina, and S28-S20 with strains from India (Y567) and Spain (AJ83), showcasing surprising mesophilic strain diversity across geographic locations. Predation tests were carried out with various mesophilic and psychrophilic strains of A. salmonicida, including Alberta isolates. The amoeba cell lines used were DH1-10 and AX2. Although the mesophilic isolates were very resistant to predation by the amoeba DH1-10, some lost this resistance to the AX2 strain, which appeared more voracious in the conditions tested. In addition, when diluting the culture medium used in a predation test with AX2, a loss of the capacity to predation resistance was observed for all the mesophilic isolates, including the highly resistant S28-S20 isolate. This study provides insights into the predation resistance of A. salmonicida isolates and offers avenues for better characterizing mesophilic isolates.","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11484801/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142344379","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Expression regulation of type III secretion system 2 in Vibrio parahaemolyticus by catabolite activator protein. 副溶血性弧菌 III 型分泌系统 2 的表达受代谢物激活蛋白的调控。

IF 2.2 4区生物学

Fems Microbiology Letters Pub Date : 2024-01-09 DOI: 10.1093/femsle/fnae054

Tomotaka Tanabe, Mitsuki Tsukamoto, Mahiro Shioda, Kenjiro Nagaoka, Tatsuya Funahashi

{"title":"Expression regulation of type III secretion system 2 in Vibrio parahaemolyticus by catabolite activator protein.","authors":"Tomotaka Tanabe, Mitsuki Tsukamoto, Mahiro Shioda, Kenjiro Nagaoka, Tatsuya Funahashi","doi":"10.1093/femsle/fnae054","DOIUrl":"10.1093/femsle/fnae054","url":null,"abstract":"Vibrio parahaemolyticus has two sets of type III secretion systems that are major pathogenic factors: T3SS1 (cytotoxicity) and T3SS2 (enterotoxicity). V. parahaemolyticus mainly colonizes the distal small intestine after oral infection and may be exposed to carbon-limiting stress due to the lack of readily available carbohydrates in this environment. Catabolite activator protein (CAP), a transcription factor involved in carbon-limiting metabolism in many Gram-negative bacteria, is well known to be involved in the regulation of the expression of many virulence factors. In this study, we determined the effects of CAP on the expression of T3SSs in this bacterium. Based on a lactate dehydrogenase-based cytotoxicity assay, CAP was found to have a greater contribution to the expression of T3SS2-dependent cytotoxicity than to that of T3SS1. Reverse transcription quantitative PCR revealed decreased expression of many T3SS2-related genes, including vpa1348, in the cap gene deletion mutant compared to the parent strain. CAP was demonstrated to bind near the T-rich elements within the vpa1348 promoter region in an electrophoretic mobility shift assay and DNase I footprinting. CAP also enhanced the expression of vpa1348 in a β-galactosidase reporter assay. Collectively, these results suggest that CAP is involved in T3SS2-mediated virulence by regulating the expression of vpa1348 in V. parahaemolyticus.","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141758081","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Analysis of CenKR essentiality in Sinorhizobium meliloti and its activity at a target gene promoter in vivo. 分析 CenKR 在瓜萎镰刀菌（sinorhizobium meliloti）中的必要性及其在体内目标基因启动子上的活性。

IF 2.2 4区生物学

Fems Microbiology Letters Pub Date : 2024-01-09 DOI: 10.1093/femsle/fnae061

Isabela R Freire, Eukene O Bensig, ZiYu Kuang, Shawn R MacLellan

{"title":"Analysis of CenKR essentiality in Sinorhizobium meliloti and its activity at a target gene promoter in vivo.","authors":"Isabela R Freire, Eukene O Bensig, ZiYu Kuang, Shawn R MacLellan","doi":"10.1093/femsle/fnae061","DOIUrl":"10.1093/femsle/fnae061","url":null,"abstract":"The two-component regulatory system CenK-CenR has recently emerged as a regulator of cell envelope and cell division processes in the alpha-proteobacteria. In Sinorhizobium meliloti, CenK-CenR regulates the expression of SrlA, a thioredoxin-domain protein of unknown function. Deletion of srlA causes sensitivity to salt and oxidizing agents on solid growth medium. In this work, we report that the response regulator CenR, but not the histidine kinase CenK, is essential for cell viability in S. meliloti. We also demonstrate that phosphorylation of the target residue D55 is not required for viability, suggesting that the unphosphorylated transcription factor sufficiently regulates expression of one or more essential genes in the genome. Using transcription assays and phenotype testing we examine CenK-CenR-dependent activation of the srlA promoter and demonstrate its absolute dependence on phosphoryl-CenR for activity and that the CenR substitution D55E acts as a phosphomimetic that partially restores activity at the srlA promoter in the absence of phosphorylation by CenK. Finally, we report a mutational analysis of the CenR binding site in the srlA promoter required for transcriptional activation.","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11328730/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141765863","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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