Archives of Microbiology最新文献

{"title":"Salt-tolerant plant growth-promoting bacteria as a versatile tool for combating salt stress in crop plants.","authors":"Xue Xie, Longzhan Gan, Chengyang Wang, Tengxia He","doi":"10.1007/s00203-024-04071-8","DOIUrl":"10.1007/s00203-024-04071-8","url":null,"abstract":"<p><p>Soil salinization poses a great threat to global agricultural ecosystems, and finding ways to improve the soils affected by salt and maintain soil health and sustainable productivity has become a major challenge. Various physical, chemical and biological approaches are being evaluated to address this escalating environmental issue. Among them, fully utilizing salt-tolerant plant growth-promoting bacteria (PGPB) has been labeled as a potential strategy to alleviate salt stress, since they can not only adapt well to saline soil environments but also enhance soil fertility and plant development under saline conditions. In the last few years, an increasing number of salt-tolerant PGPB have been excavated from specific ecological niches, and various mechanisms mediated by such bacterial strains, including but not limited to siderophore production, nitrogen fixation, enhanced nutrient availability, and phytohormone modulation, have been intensively studied to develop microbial inoculants in agriculture. This review outlines the positive impacts and growth-promoting mechanisms of a variety of salt-tolerant PGPB and opens up new avenues to commercialize cultivable microbes and reduce the detrimental impacts of salt stress on plant growth. Furthermore, considering the practical limitations of salt-tolerant PGPB in the implementation and potential integration of advanced biological techniques in salt-tolerant PGPB to enhance their effectiveness in promoting sustainable agriculture under salt stress are also accentuated.</p>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141533466","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Saccharopolyspora mangrovi sp. nov., a novel mangrove soil actinobacterium with distinct metabolic potential revealed by comparative genomic analysis.","authors":"Yi-Ting Lu, Yi-Yi Wu, Ya-Nan Li, Wei-Yi Zheng, Wen-Zheng Liu","doi":"10.1007/s00203-024-04069-2","DOIUrl":"10.1007/s00203-024-04069-2","url":null,"abstract":"<p><p>A novel mangrove soil-derived actinomycete, strain S2-29^T, was found to be most closely related to Saccharopolyspora karakumensis 5K548^T based on 16 S rRNA sequence (99.24% similarity) and genomic phylogenetic analyses. However, significant divergence in digital DNA-DNA hybridization, average nucleotide identity, and unique biosynthetic gene cluster possession distinguished S2-29^T as a distinct Saccharopolyspora species. Pan genome evaluation revealed exceptional genomic flexibility in genus Saccharopolyspora, with > 95% accessory genome content. Strain S2-29^T harbored 718 unique genes, largely implicated in energetic metabolisms, indicating different metabolic capacities from its close relatives. Several uncharacterized biosynthetic gene clusters in strain S2-29^T highlighted the strain's untapped capacity to produce novel functional compounds with potential biotechnological applications. Designation as novel species Saccharopolyspora mangrovi sp. nov. (type strain S2-29^T = JCM 34,548^T = CGMCC 4.7716^T) was warranted, expanding the known Saccharopolyspora diversity and ecology. The discovery of this mangrove-adapted strain advances understanding of the genus while highlighting an untapped source of chemical diversity.</p>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141533465","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microalgae-mediated bioremediation: current trends and opportunities-a review.","authors":"Sameh S Ali, Lamiaa H S Hassan, Mostafa El-Sheekh","doi":"10.1007/s00203-024-04052-x","DOIUrl":"10.1007/s00203-024-04052-x","url":null,"abstract":"<p><p>Environmental pollution poses a critical global challenge, and traditional wastewater treatment methods often prove inadequate in addressing the complexity and scale of this issue. On the other hand, microalgae exhibit diverse metabolic capabilities that enable them to remediate a wide range of pollutants, including heavy metals, organic contaminants, and excess nutrients. By leveraging the unique metabolic pathways of microalgae, innovative strategies can be developed to effectively remediate polluted environments. Therefore, this review paper highlights the potential of microalgae-mediated bioremediation as a sustainable and cost-effective alternative to conventional methods. It also highlights the advantages of utilizing microalgae and algae-bacteria co-cultures for large-scale bioremediation applications, demonstrating impressive biomass production rates and enhanced pollutant removal efficiency. The promising potential of microalgae-mediated bioremediation is emphasized, presenting a viable and innovative alternative to traditional treatment methods in addressing the global challenge of environmental pollution. This review identifies the opportunities and challenges for microalgae-based technology and proposed suggestions for future studies to tackle challenges. The findings of this review advance our understanding of the potential of microalgae-based technology wastewater treatment.</p>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141533464","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"High-throughput combination assay for studying biofilm formation of uropathogenic Escherichia coli.","authors":"M Li, C D Cruz, P Ilina, P Tammela","doi":"10.1007/s00203-024-04029-w","DOIUrl":"10.1007/s00203-024-04029-w","url":null,"abstract":"<p><p>Uropathogenic Escherichia coli, the most common cause for urinary tract infections, forms biofilm enhancing its antibiotic resistance. To assess the effects of compounds on biofilm formation of uropathogenic Escherichia coli UMN026 strain, a high-throughput combination assay using resazurin followed by crystal violet staining was optimized for 384-well microplate. Optimized assay parameters included, for example, resazurin and crystal violet concentrations, and incubation time for readouts. For the assay validation, quality parameters Z' factor, coefficient of variation, signal-to-noise, and signal-to-background were calculated. Microplate uniformity, signal variability, edge well effects, and fold shift were also assessed. Finally, a screening with known antibacterial compounds was conducted to evaluate the assay performance. The best conditions found were achieved by using 12 µg/mL resazurin for 150 min and 0.023% crystal violet. This assay was able to detect compounds displaying antibiofilm activity against UMN026 strain at sub-inhibitory concentrations, in terms of metabolic activity and/or biomass.</p>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11226472/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141533463","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbial allies: exploring fungal endophytes for biosynthesis of terpenoid indole alkaloids.","authors":"Jaya Prabha Khalkho, Abhishek Beck, Priyanka, Banishree Panda, Ramesh Chandra","doi":"10.1007/s00203-024-04067-4","DOIUrl":"10.1007/s00203-024-04067-4","url":null,"abstract":"<p><p>Terpenoid indole alkaloids (TIAs) are natural compounds found in medicinal plants that exhibit various therapeutic activities, such as antimicrobial, anti-inflammatory, antioxidant, anti-diabetic, anti-helminthic, and anti-tumor properties. However, the production of these alkaloids in plants is limited, and there is a high demand for them due to the increasing incidence of cancer cases. To address this research gap, researchers have focused on optimizing culture media, eliciting metabolic pathways, overexpressing genes, and searching for potential sources of TIAs in organisms other than plants. The insufficient number of essential genes and enzymes in the biosynthesis pathway is the reason behind the limited production of TIAs. As the field of natural product discovery from biological species continues to grow, endophytes are being investigated more and more as potential sources of bioactive metabolites with a variety of chemical structures. Endophytes are microorganisms (fungi, bacteria, archaea, and actinomycetes), that exert a significant influence on the metabolic pathways of both the host plants and the endophytic cells. Bio-prospection of fungal endophytes has shown the discovery of novel, high-value bioactive compounds of commercial significance. The discovery of therapeutically significant secondary metabolites has been made easier by endophytic entities' abundant but understudied diversity. It has been observed that fungal endophytes have better intermediate processing ability due to cellular compartmentation. This paper focuses on fungal endophytes and their metabolic ability to produce complex TIAs, recent advancements in this area, and addressing the limitations and future perspectives related to TIA production.</p>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141496978","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A rho-type GTPase activating protein affects the growth and development of Cordyceps cicadae.","authors":"Xueqian Li, Yu Zou, Neeraj Shrivastava, Jiandong Bao, Fu-Cheng Lin, Hongkai Wang","doi":"10.1007/s00203-024-04072-7","DOIUrl":"10.1007/s00203-024-04072-7","url":null,"abstract":"<p><p>Cordyceps cicadae is recognized for its medicinal properties, attributed to bioactive constituents like polysaccharides and adenosine, which have been shown to improve kidney and liver functions and possess anti-tumor properties. Rho GTPase activating proteins (Rho GAPs) serve as inhibitory regulators of Rho GTPases in eukaryotic cells by accelerating the GTP hydrolysis of Rho GTPases, leading to their inactivation. In this study, we explored the function of the CcRga8 gene in C. cicadae, which encodes a Rho-type GTPase activating protein. Our study found that the knockout of CcRga8 resulted in a decrease in polysaccharide levels and an increase in adenosine concentration. Furthermore, the mutants exhibited altered spore yield and morphology, fruiting body development, decreased infectivity, reduced resistance to hyperosmotic stress, oxidative conditions, and cell wall inhibitors. These findings suggest that CcRga8 plays a crucial role in the development, stress response, and bioactive compound production of C. cicadae.</p>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141490666","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Oleaginous fungi: a promising source of biofuels and nutraceuticals with enhanced lipid production strategies.","authors":"Abdallah M A Hassane, Khalifa S H Eldiehy, Debanjan Saha, Hassan Mohamed, Mohamed A Mosa, Mohamed E Abouelela, Nageh F Abo-Dahab, Abdel-Rehim A El-Shanawany","doi":"10.1007/s00203-024-04054-9","DOIUrl":"10.1007/s00203-024-04054-9","url":null,"abstract":"<p><p>Oleaginous fungi have attracted a great deal of interest for their potency to accumulate high amounts of lipids (more than 20% of biomass dry weight) and polyunsaturated fatty acids (PUFAs), which have a variety of industrial and biological applications. Lipids of plant and animal origin are related to some restrictions and thus lead to attention towards oleaginous microorganisms as reliable substitute resources. Lipids are traditionally biosynthesized intra-cellularly and involved in the building structure of a variety of cellular compartments. In oleaginous fungi, under certain conditions of elevated carbon ratio and decreased nitrogen in the growth medium, a change in metabolic pathway occurred by switching the whole central carbon metabolism to fatty acid anabolism, which subsequently resulted in high lipid accumulation. The present review illustrates the bio-lipid structure, fatty acid classes and biosynthesis within oleaginous fungi with certain key enzymes, and the advantages of oleaginous fungi over other lipid bio-sources. Qualitative and quantitative techniques for detecting the lipid accumulation capability of oleaginous microbes including visual, and analytical (convenient and non-convenient) were debated. Factors affecting lipid production, and different approaches followed to enhance the lipid content in oleaginous yeasts and fungi, including optimization, utilization of cost-effective wastes, co-culturing, as well as metabolic and genetic engineering, were discussed. A better understanding of the oleaginous fungi regarding screening, detection, and maximization of lipid content using different strategies could help to discover new potent oleaginous isolates, exploit and recycle low-cost wastes, and improve the efficiency of bio-lipids cumulation with biotechnological significance.</p>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141490665","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Crenobacter oryzisoli sp. nov., a novel phosphate-solubilizing bacterium isolated from the paddy soil.","authors":"Shu-Qun Zhang, Cheng-Jie Xie, Ling Yao, Christopher Rensing, Hao Lin, Guo-Hong Liu, Shun-Gui Zhou","doi":"10.1007/s00203-024-04070-9","DOIUrl":"10.1007/s00203-024-04070-9","url":null,"abstract":"<p><p>Two Gram-staining-negative, facultative anaerobic, rod-shaped and phosphate-solubilizing strains designated SG2303^T and SG2305, were isolated from paddy soil in China. Phylogenetic analysis based on 16 S rRNA gene sequences indicated that SG2303^T and SG2305 represented a member of the genus Crenobacter within the family Neisseriaceae of the phylum Pseudomonadota. Strain SG2303^T displayed higher 16 S rRNA gene sequence similarities with members of the genus Crenobacter ranging from 93.5 to 94.0%. Strains C. luteus YIM 78141^T and C. cavernae K1W11S-77^T were closest related to the isolated strains and were considered as type strains. Growth of strain SG2303^T occurred at 10-55 °C (optimum 37 °C), pH 5.0-9.0 (optimum pH 6.0-7.0) and 0-1% (w/v) NaCl (optimum 0%). The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain SG2303^T and its closely related taxa were 76.1-78.2% and 20.5-22.1%, respectively. The genomic DNA G + C content was 62.2%. The quinone of strain SG2303^T was Q-8. The major fatty acids (> 10%) of strain SG2303^T were C_16:0 (30.6%), summed feature 3 (C_16:1ω7c and/or C_16:1ω6c) (26.0%) and C_12:0 3OH (12.1%). The polar lipids were phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phospholipids (PL), glycolipid (GL) and unidentified lipids (UL). Based on the results of the phylogenetic, physiological, biochemical, and morphological analysis, strain SG2303^T is recognized as a novel species of the genus Crenobacter, for which the name Crenobacter oryzisoli sp. nov. is proposed. The type strain is SG2303^T (= GDMCC 1.3970^T = JCM 36468^T). In addition, SG2303^T was also able of phosphorus solubilization and promoting the growth of rice seeds. Strain SG2303^T exhibited a relatively high dissolvable phosphorus content of 2.52 µg·mL^- 1.</p>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141490663","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Isolation, whole genome sequencing and application of a broad-spectrum Salmonella phage.","authors":"Xiaofeng Zheng, Xin Wang, Yu Zhou, Meihan Liu, Pei Li, Linyun Gao, Hui Wang, Xuelian Ma, Liqun Wang, Xiang Huo, Wei Zhang","doi":"10.1007/s00203-024-04061-w","DOIUrl":"10.1007/s00203-024-04061-w","url":null,"abstract":"<p><p>Salmonella is considered as one of the most common zoonotic /foodborne pathogens in the world. The application of bacteriophages as novel antibacterial agents in food substrates has become an emerging strategy. Bacteriophages have the potential to control Salmonella contamination.We have isolated and characterized a broad-spectrum Salmonella phage, SP154, which can lyse 9 serotypes, including S. Enteritidis, S. Typhimurium, S. Pullorum, S. Arizonae, S. Dublin, S. Cholerasuis, S. Chester, S. 1, 4, [5], 12: i: -, and S. Derby, accounting for 81.9% of 144 isolates. SP154 showed a short latent period (40 min) and a high burst size (with the first rapid burst size at 107 PFUs/cell and the second rapid burst size at approximately 40 PFUs/cell). Furthermore, SP154 activity has higher survival rates across various environmental conditions, including pH 4.0-12.0 and temperatures ranging from 4 to 50 °C for 60 min, making it suitable for diverse food processing and storage applications. Significant reductions in live Salmonella were observed in different foods matrices such as milk and chicken meat, with a decrease of up to 1.9 log₁₀ CFU/mL in milk contamination and a 1 log₁₀ CFU/mL reduction in chicken meat. Whole genome sequencing analysis revealed that SP154 belongs to the genus Ithacavirus, subfamily Humphriesvirinae, within the family Schitoviridae. Phylogenetic analysis based on the terminase large subunit supported this classification, although an alternate tree using the tail spike protein gene suggested affiliation with the genus Kuttervirus, underscoring the limitations of relying on a single gene for phylogenetic inference. Importantly, no virulence or antibiotic resistance genes were detected in SP154. Our research highlights the potential of using SP154 for biocontrol of Salmonella in the food industry.</p>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141490664","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analysis of the cell wall binding domain in bacteriocin-like lysin LysL from Lactococcus lactis LAC460.","authors":"Samira Mokhtari, Yanru Li, Per E J Saris, Timo M Takala","doi":"10.1007/s00203-024-04066-5","DOIUrl":"10.1007/s00203-024-04066-5","url":null,"abstract":"<p><p>Wild-type Lactococcus lactis strain LAC460 secretes prophage-encoded bacteriocin-like lysin LysL, which kills some Lactococcus strains, but has no lytic effect on the producer. LysL carries two N-terminal enzymatic active domains (EAD), and an unknown C-terminus without homology to known domains. This study aimed to determine whether the C-terminus of LysL carries a cell wall binding domain (CBD) for target specificity of LysL. The C-terminal putative CBD region of LysL was fused with His-tagged green fluorescent protein (HGFPuv). The HGFPuv_CBDlysL gene fusion was ligated into the pASG-IBA4 vector, and introduced into Escherichia coli. The fusion protein was produced and purified with affinity chromatography. To analyse the binding of HGFPuv_CBDLysL to Lactococcus cells, the protein was mixed with LysL-sensitive and LysL-resistant strains, including the LysL-producer LAC460, and the fluorescence of the cells was analysed. As seen in fluorescence microscope, HGFPuv_CBDLysL decorated the cell surface of LysL-sensitive L. cremoris MG1614 with green fluorescence, whereas the resistant L. lactis strains LM0230 and LAC460 remained unfluorescent. The fluorescence plate reader confirmed the microscopy results detecting fluorescence only from four tested LysL-sensitive strains but not from 11 tested LysL-resistant strains. Specific binding of HGFPuv_CBDLysL onto the LysL-sensitive cells but not onto the LysL-resistant strains indicates that the C-terminus of LysL contains specific CBD. In conclusion, this report presents experimental evidence of the presence of a CBD in a lactococcal phage lysin. Moreover, the inability of HGFPuv_CBDLysL to bind to the LysL producer LAC460 may partly explain the host's resistance to its own prophage lysin.</p>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11219366/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141490662","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}