Microbial Physiology最新文献

{"title":"Optimization of Cultural Conditions for Pectinase Production by Streptomyces sp. and Characterization of Partially Purified Enzymes.","authors":"Sarita Shrestha, Chonlong Chio, Janak Raj Khatiwada, Aristide Laurel Mokale Kognou, Xuantong Chen, Wensheng Qin","doi":"10.1159/000528257","DOIUrl":"10.1159/000528257","url":null,"abstract":"<p><p>The cultural parameters of Streptomyces sp. for pectinase production were optimized using the Box-Behnken design. The maximum pectinase production was obtained after 58 h at 35°C and pH 7 upon submerged fermentation in yeast extract-containing media. The enzymes were partially purified with acetone precipitation, and the analysis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and zymogram revealed that Streptomyces sp. produced two pectinases protein with molecular weights of about 25 and 75 kDa. The pectinase activity was detected in a wide range of temperatures (30°C-80°C) and pH (3-9) with maximum pectinase activities observed at 70°C and pH 5 and 9. The enzymes retained about 30-40% of their activities even after incubating the enzyme at different temperatures for 120 min. The pectinase activities of Streptomyces sp. were enhanced in the media containing 1.5% pectin, 1% casein as a nitrogen source, 0.5 mM MgSO4, and 5 mM NaCl. Further, the addition of Tween-20, amino acids, and vitamins to the media also enhanced the pectinase activity. Moreover, the bacterium illustrated the ability to decolorize crystal violet dye efficiently. The decolorization rate ranged from 39.29 to 53.75%, showing the highest bacterial decolorization in the media containing 2 mg/mL crystal violet at 144 h. Therefore, the bacterium has the potential in treating wastewater produced by industries like textile industries.</p>","PeriodicalId":18457,"journal":{"name":"Microbial Physiology","volume":" ","pages":"12-26"},"PeriodicalIF":3.9,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40701873","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":"Polyphosphate Kinases Phosphorylate Thiamine Phosphates.","authors":"Jennie C Hildenbrand, Georg A Sprenger, Attila Teleki, Ralf Takors, Dieter Jendrossek","doi":"10.1159/000526662","DOIUrl":"10.1159/000526662","url":null,"abstract":"<p><p>Polyphosphate kinases (PPKs) catalyze the reversible transfer of the γ-phosphate moiety of ATP (or of another nucleoside triphosphate) to a growing chain of polyphosphate (polyP). In this study, we describe that PPKs of various sources are additionally able to phosphorylate thiamine diphosphate (ThP2) to produce thiamine triphosphate (ThP3) and even thiamine tetraphosphate in vitro using polyP as phosphate donor. Furthermore, all tested PPK2s, but not PPK1s, were able to phosphorylate thiamine monophosphate (ThP1) to ThP2 and ThP3 although at low efficiency. The predicted masses and identities of the mono- and oligo-phosphorylated thiamine metabolites were identified by high-performance liquid chromatography tandem mass spectrometry. Moreover, the biological activity of ThP2, that was synthesized by phosphorylation of ThP1 with polyP and PPK, as a cofactor of ThP2-dependent enzymes (here transketolase TktA from Escherichia coli) was confirmed in a coupled enzyme assay. Our study shows that PPKs are promiscuous enzymes in vitro that could be involved in the formation of a variety of phosphorylated metabolites in vivo.</p>","PeriodicalId":18457,"journal":{"name":"Microbial Physiology","volume":" ","pages":"1-11"},"PeriodicalIF":3.9,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40331484","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":"Targeted Cell Labeling and Sorting of Prokaryotes for Cultivation and Omics Approaches.","authors":"Gunnar Sturm, Mohammad Mojarrad, Anne-Kristin Kaster","doi":"10.1159/000532088","DOIUrl":"10.1159/000532088","url":null,"abstract":"<p><p>To date, the vast majority of prokaryotic organisms escapes detailed characterization because they cannot be isolated in axenic cultures. These organisms are referred to as microbial dark matter. Targeted labelling and sorting of these microorganisms pave the way for single-cell, enrichment, or cultivation approaches. In this review, we describe an array of different methods ranging from labeling-free to specific labelling techniques. In addition, different cell sorting methods and their combinations with targeting strategies are summarized and downstream applications like sequencing and cultivation are reviewed. Recent advances, challenges, and limitations of the particular methods are discussed with respect to cell viability, genome integrity as well as throughput, in order to help researchers select the most suitable methods for their specific research questions.</p>","PeriodicalId":18457,"journal":{"name":"Microbial Physiology","volume":" ","pages":"63-84"},"PeriodicalIF":3.9,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41141966","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":"Sequence Similarity among Structural Repeats in the Piezo Family of Mechanosensitive Ion Channels.","authors":"Kevin J Hendargo, Ashay O Patel, Onyeka S Chukwudozie, Gabriel Moreno-Hagelsieb, J Andres Christen, Arturo Medrano-Soto, Milton H Saier","doi":"10.1159/000531468","DOIUrl":"10.1159/000531468","url":null,"abstract":"<p><p>Members of the Piezo family of mechanically activated cation channels are involved in multiple physiological processes in higher eukaryotes, including vascular development, cell differentiation, touch perception, hearing, and more, but they are also common in single-celled eukaryotic microorganisms. Mutations in these proteins in humans are associated with a variety of diseases, such as colorectal adenomatous polyposis, dehydrated hereditary stomatocytosis, and hereditary xerocytosis. Available 3D structures for Piezo proteins show nine regions of four transmembrane segments each that have the same fold. Despite the remarkable similarity among the nine characteristic structural repeats in the family, no significant sequence similarity among them has been reported. Using bioinformatics approaches and the Transporter Classification Database (TCDB) as reference, we reliably identified sequence similarity among repeats based on four lines of evidence: (1) hidden Markov model-profile similarities across repeats at the family level, (2) pairwise sequence similarities between different repeats across Piezo homologs, (3) Piezo-specific conserved sequence signatures that consistently identify the same regions across repeats, and (4) conserved residues that maintain the same orientation and location in 3D space.</p>","PeriodicalId":18457,"journal":{"name":"Microbial Physiology","volume":" ","pages":"49-62"},"PeriodicalIF":0.1,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11283329/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9639934","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":"Characterization of Potential Virulence, Resistance to Antibiotics and Heavy Metals, and Biofilm-Forming Capabilities of Soil Lignocellulolytic Bacteria.","authors":"Aristide Laurel Mokale Kognou, Chonlong Chio, Janak Raj Khatiwada, Sarita Shrestha, Xuantong Chen, Yuen Zhu, Rosalie Anne Ngono Ngane, Gabriel Agbor Agbor, Zi-Hua Jiang, Chunbao Charles Xu, Wensheng Qin","doi":"10.1159/000530228","DOIUrl":"10.1159/000530228","url":null,"abstract":"<p><p>Soil bacteria participate in self-immobilization processes for survival, persistence, and production of virulence factors in some niches or hosts through their capacities for autoaggregation, cell surface hydrophobicity, biofilm formation, and antibiotic and heavy metal resistance. This study investigated potential virulence, antibiotic and heavy metal resistance, solvent adhesion, and biofilm-forming capabilities of six cellulolytic bacteria isolated from soil samples: Paenarthrobacter sp. MKAL1, Hymenobacter sp. MKAL2, Mycobacterium sp. MKAL3, Stenotrophomonas sp. MKAL4, Chryseobacterium sp. MKAL5, and Bacillus sp. MKAL6. Strains were subjected to phenotypic methods, including heavy metal and antibiotic susceptibility and virulence factors (protease, lipase, capsule production, autoaggregation, hydrophobicity, and biofilm formation). The effect of ciprofloxacin was also investigated on bacterial susceptibility over time, cell membrane, and biofilm formation. Strains MKAL2, MKAL5, and MKAL6 exhibited protease and lipase activities, while only MKAL6 produced capsules. All strains were capable of aggregating, forming biofilm, and adhering to solvents. Strains tolerated high amounts of chromium, lead, zinc, nickel, and manganese and were resistant to lincomycin. Ciprofloxacin exhibited bactericidal activity against these strains. Although the phenotypic evaluation of virulence factors of bacteria can indicate their pathogenic nature, an in-depth genetic study of virulence, antibiotic and heavy metal resistance genes is required.</p>","PeriodicalId":18457,"journal":{"name":"Microbial Physiology","volume":" ","pages":"36-48"},"PeriodicalIF":3.9,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9156717","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":"Bacterial Diversity and Community Structure of the Jujube Rhizosphere in Southern Xinjiang Uygur Autonomous Region, China","authors":"Zhaoyang Liu, Bingcong Ji, Yaqing Zhang, Xunli Liu","doi":"10.1159/000525000","DOIUrl":"https://doi.org/10.1159/000525000","url":null,"abstract":"Jujube is an important economic crop in the Xinjiang Uygur Autonomous Region. Microbial diversity in the rhizosphere is essential for plant quality; however, soil bacterial diversity and community structure in the jujube rhizosphere have not been characterized in this region. In this study, we used pyrosequencing to analyze bacterial diversity and community structure at different growth stages in the jujube rhizosphere in Hetian, Kashi, and Aksu prefectures. These results revealed a greater bacterial diversity in the 8-year jujube rhizosphere as compared with the 3-year-old rhizosphere taken from the same sampling area. Moreover, samples obtained from Kashi prefecture showed the largest diversity among the different areas. The most abundant phyla across all soil samples were Proteobacteria, Actinobacteria, Acidobacteria, Bacteroidetes, and Firmicutes. Dominant phyla in the 8-year jujube rhizosphere accounted for the increased observed diversity. Furthermore, comparative analysis of the bacterial communities with respect to rhizosphere age and sampling areas revealed a significant correlation between soil properties and phyla diversity. To the best of our knowledge, this is the first study of jujube rhizosphere bacterial diversity and community structure in the southern Xinjiang Uygur Autonomous Region, and we hope that our research provides a reference for future studies.","PeriodicalId":18457,"journal":{"name":"Microbial Physiology","volume":"32 1","pages":"135 - 145"},"PeriodicalIF":3.9,"publicationDate":"2022-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42646204","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":"Nanomolar Responsiveness of Marine Phaeobacter inhibens DSM 17395 toward Carbohydrates and Amino Acids","authors":"Arne Weiten, K. Kalvelage, Meina Neumann-Schaal, Ramona Buschen, Sabine Scheve, M. Winklhofer, R. Rabus","doi":"10.1159/000524702","DOIUrl":"https://doi.org/10.1159/000524702","url":null,"abstract":"Phaeobacter inhibens DSM 17395 is a heterotrophic member of the ubiquitous, marine Roseobacter group and specializes in the aerobic utilization of carbohydrates and amino acids via pathways widespread among roseobacters. The in vivo responsiveness of P. inhibens DSM 17395 was studied with nonadapted cells (succinate-grown), which were exposed to a single pulse (100–0.01 µM) each of N-acetylglucosamine, mannitol, xylose, leucine, phenylalanine, or tryptophan (effectors). Responsiveness was then determined by time-resolved transcript analyses (quantitative reverse transcription-PCR) of “degradation” and “uptake” genes selected based on previously reported substrate-specific proteome profiles. The transcriptional response thresholds were: 50–100 nM for nagK (N-acetylglucosamine kinase), paaA (ring 1,2-phenylacetyl-CoA epoxidase), and kynA (tryptophan 2,3-dioxygenase), 10–50 nM for xylA (xylose isomerase), and around 10 nM for mtlK (mannitol 2-dehydrogenase). A threshold for leucine could not be determined due to the elevated intrinsic presence of leucine in the exometabolome of succinate-grown cells (no effector addition). Notably, the response thresholds for presumptive carbohydrate-binding proteins of ABC-transporters were in the same range or even lower: 0.1–1 µM for c27930 (N-acetylglucosamine) and even below 10 nM for c13210 (mannitol) and xylF (xylose). These results shed new light on the sensory/regulatory sensitivity of a well-studied roseobacter for recognizing potential substrates at low ambient concentrations and on the concentration threshold below which these might escape biodegradation (“emergent recalcitrance” concept of dissolved organic matter persistence).","PeriodicalId":18457,"journal":{"name":"Microbial Physiology","volume":"32 1","pages":"108 - 121"},"PeriodicalIF":3.9,"publicationDate":"2022-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49384769","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":"Interplay between the Conserved Pore Residues Thr-91 and His-209 Controls Formate Translocation through the FocA Channel","authors":"Michelle Kammel, Oliver Trebbin, R. Sawers","doi":"10.1159/000524454","DOIUrl":"https://doi.org/10.1159/000524454","url":null,"abstract":"The formate channel A (FocA) belongs to the formate-nitrite transporter (FNT) family, members of which permeate small monovalent anions. FocA from Escherichia coli translocates formate/formic acid bi-directionally across the cytoplasmic membrane during fermentative growth. Two residues are particularly well-conserved within the translocation pores of FNTs: threonine-91 and histidine-209, based on E. coli FocA numbering. These residues are located at the tips of two broken transmembrane helices and control anion passage. H209 is the only charged residue within the pore and interacts with T91. Here, we addressed the role of the T91-H209 interaction network in the permeation of formate in vivo through FocA by performing an extensive amino acid-exchange study. Monitoring changes in intracellular formate using a formate-responsive fdhFP::lacZ reporter system revealed that T91 is essential for the ability of FocA to translocate formate bi-directionally. Only exchange for serine was partially tolerated, indicating that the hydroxyl group of T91 is mechanistically important. Substitution of H209 with N or Q was previously shown to convert FocA into a formate efflux channel. We show here that residue exchanges A, I, and T at this position resulted in a similar phenotype. Moreover, efflux function was confirmed for these FocA variants by measuring excreted formate in the culture medium. Substitution of bulky or charged residues for H209 prevented bi-directional formate passage. Studies using hypophosphite, a toxic analogue of formate taken up by FocA, and which causes impaired growth, confirmed that T91 and H209 substitutions essentially abolished, or drastically reduced, FocA’s translocation activity, as shown by effects on growth rate. The exceptions were T91S- and T91Y-exchange variants that retained partial ability to take up inhibitory hypophosphite. Together, our findings indicate that T91 is essential for formate permeation in both directions; however, it is particularly important to allow anion efflux. Moreover, H209 is essential for formate uptake by FocA, strongly suggesting that protonation-deprotonation of this residue plays a role in formate uptake. Finally, our results substantiate the premise that efflux and influx of formate by FocA are mechanistically distinct processes that are controlled by the interplay between T91 and H209.","PeriodicalId":18457,"journal":{"name":"Microbial Physiology","volume":"32 1","pages":"95 - 107"},"PeriodicalIF":3.9,"publicationDate":"2022-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46537778","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":"Acknowledgement to Reviewers","authors":"","doi":"10.1159/000520900","DOIUrl":"https://doi.org/10.1159/000520900","url":null,"abstract":"© 2022 The Author(s) Published by S. Karger AG, Basel Karger Publishers and the editors of Microbial Physiology would like to thank the reviewers for the ongoing support in reviewing manuscripts for our Journal in 2021. This year we have chosen not to disclose the names of our reviewers to preserve the principle of anonymity inherent to the single-blind peer-review we follow. Even so, this should not be in our way to sincerely thank all contributing reviewers who have volunteered their time, effort, and expertise in benefit of the quality of the manuscripts we received and published in 2021. Individual reviewers can still claim their personal “Certificate of Review” via the Journal’s manuscript submission system.”","PeriodicalId":18457,"journal":{"name":"Microbial Physiology","volume":"32 1","pages":"1 - 1"},"PeriodicalIF":3.9,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42940527","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":"Luciferase-Based Determination of ATP/NAD(H) Pools in a Marine (Environmental) Bacterium","authors":"Daniel Wünsch, Sabine Scheve, Arne Weiten, K. Kalvelage, R. Rabus","doi":"10.1159/000522414","DOIUrl":"https://doi.org/10.1159/000522414","url":null,"abstract":"In all living organisms, adenosine triphosphate (ATP) and NAD(H) represent universal molecular currencies for energy and redox state, respectively, and are thus widely applicable molecular proxies for an organism’s viability and activity. To this end, corresponding luciferase-based assays in combination with a microplate reader were established with the marine model bacterium Phaeobacter inhibens DSM 17395 (Escherichia coli K12 served as reference). Grey multiwell plates best balanced sensitivity and crosstalk, and optimal incubation times were 5 min and 30 min for the ATP and NAD(H) assay, respectively, together allowing limits of detection of 0.042, 0.470 and 0.710 nM for ATP, NAD+, and NADH, respectively. Quenching of bacterial cell samples involved Tris-EDTA-DTAB and bicarbonate base-DTAB for ATP and NAD(H) assays, respectively. The ATP and NAD(H) yields determined for P. inhibens DSM 17395 at ¼ ODmax were found to reside well within the range previously reported for E. coli and other bacteria, e.g., 3.28 µmol ATP (g cellsdry)−1. Thus, the here described methods for luciferase-based determination of ATP/NAD(H) pools open a promising approach to investigate energy and redox states in marine (environmental) bacteria.","PeriodicalId":18457,"journal":{"name":"Microbial Physiology","volume":"32 1","pages":"122 - 134"},"PeriodicalIF":3.9,"publicationDate":"2022-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48395045","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}