Fems Microbiology Letters最新文献

{"title":"Microbial chemolithoautotrophs are abundant in salt marsh sediment following long-term experimental nitrate enrichment.","authors":"Joseph H Vineis,&nbsp;Ashley N Bulseco,&nbsp;Jennifer L Bowen","doi":"10.1093/femsle/fnad082","DOIUrl":"10.1093/femsle/fnad082","url":null,"abstract":"<p><p>Long-term anthropogenic nitrate (NO3-) enrichment is a serious threat to many coastal systems. Nitrate reduction coupled with the oxidation of reduced forms of sulfur is conducted by chemolithoautotrophic microbial populations in a process that decreases nitrogen (N) pollution. However, little is known about the diversity and distribution of microbes capable of carbon fixation within salt marsh sediment and how they respond to long-term NO3- loading. We used genome-resolved metagenomics to characterize the distribution, phylogenetic relationships, and adaptations important to microbial communities within NO3--enriched sediment. We found NO3- reducing sulfur oxidizers became dominant members of the microbial community throughout the top 25 cm of the sediment following long-term NO3- enrichment. We also found that most of the chemolithoautotrophic genomes recovered contained striking metabolic versatility, including the potential for complete denitrification and evidence of mixotrophy. Phylogenetic reconstruction indicated that similar carbon fixation strategies and metabolic versatility can be found in several phylogenetic groups, but the genomes recovered here represent novel organisms. Our results suggest that the role of chemolithoautotrophy within NO3--enriched salt marsh sediments may be quantitatively more important for retaining carbon and filtering NO3- than previously indicated and further inquiry is needed to explicitly measure their contribution to carbon turnover and removal of N pollution.</p>","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2023-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10457086","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}

{"title":"A rapid and sensitive triplex-recombinase polymerase amplification for simultaneous differentiation of Brucella abortus, Brucella melitensi s, and Brucella suis in sera and foods.","authors":"Jiang Chang,&nbsp;Xusen Hou,&nbsp;Xin Yang,&nbsp;Shi-Jun Zhang,&nbsp;De-Ying Zou,&nbsp;Feng Li,&nbsp;Ying Zhang,&nbsp;Yan-Song Li,&nbsp;Shi-Ying Lu,&nbsp;Pan Hu,&nbsp;Zeng-Shan Liu,&nbsp;Hong-Lin Ren","doi":"10.1093/femsle/fnad056","DOIUrl":"https://doi.org/10.1093/femsle/fnad056","url":null,"abstract":"<p><p>Brucella is the causative agent of brucellosis and can be transmitted to humans through aerosolized particles or contaminated food. Brucella abortus (B. abortus), Brucella melitensis (B. melitensis), and Brucella suis (B. suis) are the most virulent of the brucellae, but the traditional detection methods to distinguish them are time-consuming and require high instrumentation. To obtain epidemiological information on Brucella during livestock slaughter and food contamination, we developed a rapid and sensitive triplex recombinant polymerase amplification (triplex-RPA) assay that can simultaneously detect and differentiate between B. abortus, B. melitensis, and B. suis. Three pairs of primers (B1O7F/B1O7R, B192F/B192R, and B285F/B285R) were designed and screened for the establishment of the triplex-RPA assay. After optimization, the assay can be completed within 20 min at 39°C with good specificity and no cross-reactivity with five common pathogens. The triplex-RPA assay has a DNA sensitivity of 1-10 pg and a minimum detection limit of 2.14 × 104-2.14 × 105 CFU g-1 in B. suis spiked samples. It is a potential tool for the detection of Brucella and can effectively differentiate between B. abortus, B. melitensis, and B. suis S2, making it a useful tool for epidemiological investigations.</p>","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2023-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9692357","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}

{"title":"Wide substrate range for a candidate bioremediation enzyme isolated from Nocardioides sp. strain SG-4 G.","authors":"Kishore K Krishnani,&nbsp;John G Oakeshott,&nbsp;Gunjan Pandey","doi":"10.1093/femsle/fnad085","DOIUrl":"https://doi.org/10.1093/femsle/fnad085","url":null,"abstract":"<p><p>Narrow substrate ranges can impact heavily on the range of applications and hence commercial viability of candidate bioremediation enzymes. Here we show that an ester hydrolase from Nocardioides strain SG-4 G has potential as a bioremediation agent against various pollutants that can be detoxified by hydrolytic cleavage of some carboxylester, carbamate, or amide linkages. Previously we showed that a radiation-killed, freeze-dried preparation (ZimA) of this strain can rapidly degrade the benzimidazole fungicide carbendazim due to the activity of a specific ester hydrolase, MheI. Here, we report that ZimA also has substantial hydrolytic activity against phthalate diesters (dimethyl, dibutyl, and dioctyl phthalate), anilide (propanil and monalide), and carbamate ester (chlorpropham) herbicides under laboratory conditions. The reaction products are substantially less toxic, or inactive as herbicides, than the parent compounds. Tests of strain SG-4 G and Escherichia coli expressing MheI found they were also able to hydrolyse dimethyl phthalate, propanil, and chlorpropham, indicating that MheI is principally responsible for the above activities.</p>","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2023-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10501498/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10251231","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}

{"title":"Correction to: The microbiome of the sponge Aplysina caissara in two sites with different levels of anthropogenic impact.","authors":"","doi":"10.1093/femsle/fnad094","DOIUrl":"https://doi.org/10.1093/femsle/fnad094","url":null,"abstract":"This study revealed that local anthropogenic impact altered the microbiome of the marine sponge Aplysina caissara. However, the microbiome was assembly by deterministic processes, independently of the local pollution, largely showing the pivotal rule of the sponge host.","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2023-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41120859","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}

{"title":"Empowering learning.","authors":"Beatrix Fahnert","doi":"10.1093/femsle/fnad104","DOIUrl":"10.1093/femsle/fnad104","url":null,"abstract":"","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2023-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49676043","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}

{"title":"Effect of long-term oral glutathione supplementation on gut microbiome of type 2 diabetic individuals.","authors":"Akshay H Gaike, Saurabh D Kalamkar, Vijay Gajjar, Uma Divate, Sucheta Karandikar-Iyer, Pranay Goel, Yogesh S Shouche, Saroj S Ghaskadbi","doi":"10.1093/femsle/fnad116","DOIUrl":"10.1093/femsle/fnad116","url":null,"abstract":"<p><p>The aim of this study was to check the effect of long-term oral glutathione (GSH) supplementation on alteration in gut microbiome of Indian diabetic individuals. Early morning fresh stool sample of diabetic individuals recruited in a randomized clinical trial wherein they were given 500 mg GSH supplementation orally once a day for a period of 6 months was collected and gut microbiome was analysed using high throughput 16S rRNA metagenomic sequencing. Long-term GSH supplementation as reported in our earlier work showed significant increase in body stores of GSH and stabilized decreased glycated haemoglobin (HbA1c). Analysis of gut microbiome revealed that abundance of phylum Proteobacteria significantly decreased (P < 0.05) in individuals with GSH supplementation after 6 months compared to those without it. Beneficial dominant genera such as Megasphaera, Bacteroides, and Megamonas were found to be significantly enriched (P < 0.05), while pathogenic Escherichia/Shigella was found to be depleted (P < 0.05) after supplementation. Data clearly demonstrate that GSH supplementation along with antidiabetic treatment helps restore the gut microbiome by enriching beneficial bacteria of healthy gut and reducing significantly the load of pathogenic bacteria of diabetic gut.</p>","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2023-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71479879","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}

{"title":"Isolation and identification of specific lytic bacteriophages as a biocontrol agent against Serratia odorifera PBA-IAUF-1 and Kluyvera intermedia PBA-IAUF-6 causing bacterial canker in the grape and Siberian pear.","authors":"Somayeh Parsafar, Keivan Beheshti Maal, Hamid Reza Akkafi, Ladan Rahimzadeh Torabi","doi":"10.1093/femsle/fnad115","DOIUrl":"10.1093/femsle/fnad115","url":null,"abstract":"<p><p>Bacterial canker, a prevalent disease among fruit trees, is a significant concern. The use of phage therapy is presently seen as a dependable biological strategy to control bacterial diseases in fruits. The objective of this research was to use various biochemical and molecular techniques to determine the types of bacteria responsible for causing cankers in various fruits. Additionally, their ability to cause disease in the fruit tissues was assessed, the specific bacteriophages targeting these bacteria were isolated and identified. The bacteria were separated from different parts of the infected fruits like grapes and Siberian pears. The selection of fruit tissues showing signs of canker disease was performed, and the validation of the isolates' pathogenicity was confirmed following Koch's principles. Subsequently, in order to establish a conclusive identification of the bacterial species, molecular identification was conducted through the sequencing of a specific fragment within the 16S rRNA following amplification by PCR by using universal primers, RW01 and DG74. Isolation and titration of phages specific to fruit spoilage bacteria was done by spot and double-layer agar method, and the growth curve of the isolated bacteriophage was drawn. The phages were detected by transmission electron microscopy (TEM). The results of the study proved the presence of canker causing agents, Kluyvera intermedia PBA-IAUF-6 with the code Sh6 in the Siberian pears, and Serratia odorifera PBA-IAUF-1 with the code Rz3 in the grape fruits, which were deposited in GenBank with the accession numbers of KU878579 and KU168605, respectively. Isolation of the specific bacteriophages to the S. odorifera PBA-IAUF-1 and K. intermedia PBA-IAUF-6 bacterial strains were done from the effluent of South Isfahan wastewater treatment plant and Caspian Sea water, respectively. The titer of the specific phage to S. odorifera PBA-IAUF-1 and K. intermedia PBA-IAUF-6 was detected in the samples as 2.2 × 10-5 and 5 × 10-11 PFU/ml, respectively. An electron micrograph of a bacteriophage that targets two different bacterial strains revealed phages with a geometrically shaped head and a flexible tail, which resembled viruses from the Siphoviridae family.</p>","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2023-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71479880","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}

{"title":"Real-Lab-Day: undergraduate scientific hands-on activity as an authentic learning opportunity in microbiology education.","authors":"Ana Carolina Ramos Moreno,&nbsp;Natalia Pasternak Taschner,&nbsp;Marco Aurélio Floriano Piantola,&nbsp;Bárbara Rodrigues Cintra Armellini,&nbsp;Camilo Lellis-Santos,&nbsp;Rita de Cássia Café Ferreira","doi":"10.1093/femsle/fnad062","DOIUrl":"https://doi.org/10.1093/femsle/fnad062","url":null,"abstract":"<p><p>Traditional lab classes in microbiology are common in several educational institutions, which can provide a learning experience disconnected from the myriad of experiments performed in research laboratories. Attempting to promote an authentic learning opportunity of the functioning of a bacteriology research laboratory, we developed the \"Real-Lab-Day,\" a multimodal learning experience to develop competencies, abilities, critical analysis, and teamwork skills for undergraduate students. Students were divided into groups and assigned to research laboratories to be mentored by graduate students, to design and carry out scientific assays. Undergraduate students were introduced to methods such as cellular and molecular assays, flow cytometry, and fluorescence microscopy, as tools to address scientific questions about bacterial pathogenicity, bacterial resistance, and other topics. To consolidate their learning, students created and presented a poster in a rotational panel of peer learning. The perceived learning and interest in microbiology research were improved by the Real-Lab-Day experience, and >95% of the students approved the Real-Lab-Day as a teaching tool in microbiology. Students exposed to a research laboratory had a positive experience with the teaching method, and over 90% saw it as beneficial to improve their understanding of the scientific concepts discussed during lectures. Likewise, their interest in pursuing a career in microbiology was stimulated by the Real-Lab-Day experience. In conclusion, this educational initiative depicts an alternative methodology to connect students to the research and offers an opportunity to be in close contact with experts and graduate students, who gain teaching experience.</p>","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2023-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9800500","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}

{"title":"Glycosylated proteins in the protozoan alga Euglena gracilis: a proteomic approach.","authors":"Ellis C O'Neill","doi":"10.1093/femsle/fnac120","DOIUrl":"https://doi.org/10.1093/femsle/fnac120","url":null,"abstract":"<p><p>Protein glycosylation, and in particular N-linked glycans, is a hallmark of eukaryotic cells and has been well-studied in mammalian cells and parasites. However, little research has been conducted to investigate the conservation and variation of protein glycosylation pathways in other eukaryotic organisms. Euglena gracilis is an industrially important microalga, used in the production of biofuels and nutritional supplements. It is evolutionarily highly divergent from green algae and more related to kinetoplastid pathogens. It was recently shown that E. gracilis possesses the machinery for producing a range of protein glycosylations and make simple N-glycans, but the modified proteins were not identified. This study identifies the glycosylated proteins, including transporters, extracellular proteases, and those involved in cell surface signalling. Notably, many of the most highly expressed and glycosylated proteins are not related to any known sequences and are, therefore, likely to be involved in important novel functions in Euglena.</p>","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2023-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10038220/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9184051","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}

{"title":"Constructing recombinant Saccharomyces cerevisiae strains for malic-to-fumaric acid conversion.","authors":"Annica Steyn,&nbsp;Marinda Viljoen-Bloom,&nbsp;Willem Heber Van Zyl","doi":"10.1093/femsle/fnad003","DOIUrl":"https://doi.org/10.1093/femsle/fnad003","url":null,"abstract":"<p><p>Saccharomyces cerevisiae with its robustness and good acid tolerance, is an attractive candidate for use in various industries, including waste-based biorefineries where a high-value organic acid is produced, such as fumaric acid could be beneficial. However, this yeast is not a natural producer of dicarboxylic acids, and genetic engineering of S. cerevisiae strains is required to achieve this outcome. Disruption of the natural FUM1 gene and the recombinant expression of fumarase and malate transporter genes improved the malic acid-to-fumaric acid conversion by engineered S. cerevisiae strains. The efficacy of the strains was significantly influenced by the source of the fumarase gene (yeast versus bacterial), the presence of the XYNSEC signal secretion signal and the available oxygen in synthetic media cultivations. The ΔFUM1Ckr_fum + mae1 and ΔFUM1(ss)Ckr_fum + mae1 strains converted extracellular malic acid into 0.98 and 1.11 g/L fumaric acid under aerobic conditions.</p>","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2023-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10086307/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9656478","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}