-
Journal of Microbiology & Biology... Apr 2024Nicotine is a major alkaloid in tobacco plants and an addictive component of tobacco products. Some bacteria grow on tobacco plants and have evolved the ability to...
Nicotine is a major alkaloid in tobacco plants and an addictive component of tobacco products. Some bacteria grow on tobacco plants and have evolved the ability to metabolize nicotine. As part of our microbiology teaching lab, we used minimal media with nicotine as the sole carbon source to isolate nicotine-degrading bacteria from tobacco leaves and commercial tobacco products. Students then identified these bacteria using 16S rRNA sequencing and biochemical assays and assessed their ability to catabolize nicotine using UV spectroscopy. Students were able to isolate and identify 14 distinct genera that can metabolize nicotine. This modification of the commonly used unknown project gave students firsthand experience using selective media, and students got the opportunity to work with largely uncharacterized microbes with a real-world connection to public health, which increased student engagement. Students had the opportunity to think critically about why nicotine-degrading microorganisms associate with tobacco plants, why there are different bacteria that use the same specialized metabolism, and how these organisms are isolated from other bacteria using selective media.
PubMed: 38602406
DOI: 10.1128/jmbe.00152-23 -
MicroPublication Biology 2024Enzymes combat bacterial infections by degrading biomolecules to disperse biofilms. Commercial enzyme mixtures, like cellulase and pepsin, show concentration-dependent...
Enzymes combat bacterial infections by degrading biomolecules to disperse biofilms. Commercial enzyme mixtures, like cellulase and pepsin, show concentration-dependent dispersion, but low concentrations lack synergy. Only the sequential addition of pepsin followed by zymolyase 20T displays synergy, effectively dispersing biofilms. Purified zymolyase 100T outperforms zymolyase 20T but lacks synergy with pepsin. This study underscores the complexity of enzymatic biofilm dispersal, highlighting the need for tailored approaches based on enzyme properties and biofilm composition.
PubMed: 38596361
DOI: 10.17912/micropub.biology.001119 -
Frontiers in Bioscience (Landmark... Mar 2024Bacterial endophytic communities associated with medicinal plants synthesize a plethora of bioactive compounds with biological activities. Their easy isolation and...
BACKGROUND
Bacterial endophytic communities associated with medicinal plants synthesize a plethora of bioactive compounds with biological activities. Their easy isolation and growth procedures make bacterial endophytes an untapped source of novel drugs, which might help to face the problem of antimicrobial resistance. This study investigates the antagonistic potential of endophytic bacteria isolated from different compartments of the medicinal plant against human opportunistic pathogens.
METHODS
A panel of endophytes was employed in cross-streaking tests against multidrug-resistant human pathogens, followed by high-resolution chemical profiling using headspace-gas chromatography/mass spectrometry.
RESULTS
Endophytic bacteria exhibited the ability to antagonize the growth of opportunistic pathogens belonging to the complex (Bcc). The different inhibition patterns observed were related to their taxonomic attribution at the genus level; most active strains belong to the Gram-positive genera , and . Bcc strains of clinical origin were more sensitive than environmental strains. Cross-streaking tests against other 36 human multidrug-resistant pathogens revealed the highest antimicrobial activity towards the Coagulase-negative staphylococci and strains. Interestingly, strains of human origin were the most inhibited, in both groups. Concerning the production of volatile organic compounds (VOCs), the strain sp. OHL24 was the best producer of such compounds, while two strains were good ketones producers and so could be considered for further biotechnological applications.
CONCLUSIONS
Overall, this study highlights the diverse antagonistic activities of -associated endophytes against both Bcc and multidrug-resistant (MDR) human pathogens. These findings hold important implications for investigating bacterial endophytes of medicinal plants as new sources of antimicrobial compounds.
Topics: Humans; Plants, Medicinal; Endophytes; Origanum; Bacteria; Anti-Bacterial Agents
PubMed: 38538270
DOI: 10.31083/j.fbl2903111 -
Cell Reports Apr 2024Sorghum bicolor is among the most important cereals globally and a staple crop for smallholder farmers in sub-Saharan Africa. Approximately 20% of sorghum yield is lost...
Sorghum bicolor is among the most important cereals globally and a staple crop for smallholder farmers in sub-Saharan Africa. Approximately 20% of sorghum yield is lost annually in Africa due to infestation with the root parasitic weed Striga hermonthica. Existing Striga management strategies are not singularly effective and integrated approaches are needed. Here, we demonstrate the functional potential of the soil microbiome to suppress Striga infection in sorghum. We associate this suppression with microbiome-mediated induction of root endodermal suberization and aerenchyma formation and with depletion of haustorium-inducing factors, compounds required for the initial stages of Striga infection. We further identify specific bacterial taxa that trigger the observed Striga-suppressive traits. Collectively, our study describes the importance of the soil microbiome in the early stages of root infection by Striga and pinpoints mechanisms of Striga suppression. These findings open avenues to broaden the effectiveness of integrated Striga management practices.
Topics: Sorghum; Striga; Plant Roots; Microbiota; Soil Microbiology; Metabolome; Plant Diseases
PubMed: 38537644
DOI: 10.1016/j.celrep.2024.113971 -
Marine Drugs Feb 2024Sulfation is gaining increased interest due to the role of sulfate in the bioactivity of many polysaccharides of marine origin. Hence, sulfatases, enzymes that control...
Sulfation is gaining increased interest due to the role of sulfate in the bioactivity of many polysaccharides of marine origin. Hence, sulfatases, enzymes that control the degree of sulfation, are being more extensively researched. In this work, a novel sulfatase (SulA1) encoded by the gene was characterized. The -gene is located upstream of a chondroitin lyase encoding gene in the genome of the marine Arthrobacter strain (MAT3885). The sulfatase was produced in . Based on the primary sequence, the enzyme is classified under sulfatase family 1 and the two catalytic residues typical of the sulfatase 1 family-Cys57 (post-translationally modified to formyl glycine for function) and His190-were conserved. The enzyme showed increased activity, but not improved stability, in the presence of Ca, and conserved residues for Ca binding were identified (Asp17, Asp18, Asp277, and Asn278) in a structural model of the enzyme. The temperature and pH activity profiles (screened using -nitrocatechol sulfate) were narrow, with an activity optimum at 40-50 °C and a pH optimum at pH 5.5. The was significantly higher (67 °C) than the activity optimum. Desulfation activity was not detected on polymeric substrates, but was found on GalNAc4S, which is a sulfated monomer in the repeated disaccharide unit (GlcA-GalNAc4S) of, e.g., chondroitin sulfate A. The position of the sulA1 gene upstream of a chondroitin lyase gene and combined with the activity on GalNAc4S suggests that there is an involvement of the enzyme in the chondroitin-degrading cascade reaction, which specifically removes sulfate from monomeric GalNAc4S from chondroitin sulfate degradation products.
Topics: Sulfates; Acetylgalactosamine; Arthrobacter; Sulfatases; Escherichia coli; Galactosamine; Chondroitin Lyases; Cloning, Molecular
PubMed: 38535445
DOI: 10.3390/md22030104 -
AIMS Microbiology 2024Desert soil hosts many microorganisms, whose activities are essential from an ecological viewpoint. Moreover, they are of great anthropic interest. The knowledge of...
Desert soil hosts many microorganisms, whose activities are essential from an ecological viewpoint. Moreover, they are of great anthropic interest. The knowledge of extreme environments microbiomes may be beneficial for agriculture, technology, and human health. In this study, 11 strains from topsoil samples collected from the Great Gobi A Strictly Protected Area in the Gobi Desert, were characterized by a combination of different techniques. The phylogenetic analysis, performed using their 16S rDNA sequences and the most similar sequences found in databases, revealed that most of them were close to , while others joined a sister group to the clade formed by , and . The resistance of each strain to different antibiotics, heavy-metals, and NaCl was also tested as well as the inhibitory potential against human pathogens (i.e., ssp., , and ssp.) via cross-streaking, to check the production of metabolites with antimicrobial activity. Data obtained revealed that all strains were resistant to heavy metals and were able to strongly interfere with the growth of many of the human pathogens tested. The volatile organic compounds (VOCs) profile of the 11 strains was also analyzed. A total of 16 different metabolites were found, some of which were already known for having an inhibitory action against different Gram-positive and Gram-negative bacteria. Isolate MS-3A13, producing the highest quantity of VOCs, is the most efficient against complex (Bcc), , and coagulase-negative Staphylococci (CoNS) strains. This work highlights the importance of understanding microbial populations' phenotypical characteristics and dynamics in extreme environments to uncover the antimicrobial potential of new species and strains.
PubMed: 38525036
DOI: 10.3934/microbiol.2024009 -
Microbiology Resource Announcements Apr 2024In the present work, we present the draft genome sequence of a new putative species associated with the tomato rhizosphere.
In the present work, we present the draft genome sequence of a new putative species associated with the tomato rhizosphere.
PubMed: 38517186
DOI: 10.1128/mra.01220-23 -
PeerJ 2024Biochar amendments enhance crop productivity and improve agricultural quality. To date, studies on the correlation between different amounts of biochar in pakchoi ( L.)...
BACKGROUND
Biochar amendments enhance crop productivity and improve agricultural quality. To date, studies on the correlation between different amounts of biochar in pakchoi ( L.) quality and rhizosphere soil microorganisms are limited, especially in weakly alkaline soils. The experiment was set up to explore the effect of different concentrations of biochar on vegetable quality and the correlation between the index of quality and soil bacterial community structure changes.
METHODS
The soil was treated in the following ways via pot culture: the blank control (CK) without biochar added and with biochar at different concentrations of 1% (T1), 3% (T2), 5% (T3), and 7% (T4). Here, we investigatedthe synergistic effect of biochar on the growth and quality of pakchoi, soil enzymatic activities, and soil nutrients. Microbial communities from pakchoi rhizosphere soil were analyzed by Illumina MiSeq.
RESULTS
The results revealed that adding 3% biochar significantly increased plant height, root length, and dry weight of pakchoi and increased the contents of soluble sugars, soluble proteins, Vitamin C (VC), cellulose, and reduced nitrate content in pakchoi leaves. Meanwhile, soil enzyme activities and available nutrient content in rhizosphere soil increased. This study demonstrated that the the microbial community structure of bacteria in pakchoi rhizosphere soil was changed by applying more than 3% biochar. Among the relatively abundant dominant phyla, , , and were reduced, and , , , and relative abundance increased. Furthermore, adding 3% biochar reduced the relative abundance of s and increased the relative abundances of , , , , and . The nitrate content was positively correlated with the abundance of and the nitrate content was significantly negatively correlated with the relative abundance of . Carbohydrate transport and metabolism in the rhizosphere soil of pakchoi decreased, and lipid transport and metabolism increased after biochar application.
CONCLUSION
Overall, our results indicated that applying biochar improved soil physicochemical states and plant nutrient absorption, and affected the abundance of dominant bacterial groups (, and ), these were the main factors to increase pakchoi growth and promote quality of pakchoi. Therefore, considering the growth, quality of pakchoi, and soil environment, the effect of using 3% biochar is better.
Topics: Soil; Rhizosphere; Nitrates; Soil Microbiology; Microbiota; Bacteria; Plants; Charcoal
PubMed: 38515457
DOI: 10.7717/peerj.16733 -
ISME Communications Jan 2024Northern peatlands contain ~30% of terrestrial carbon (C) stores, but in recent decades, 14% to 20% of the stored C has been lost because of conversion of the peatland...
Northern peatlands contain ~30% of terrestrial carbon (C) stores, but in recent decades, 14% to 20% of the stored C has been lost because of conversion of the peatland to cropland. Microorganisms are widely acknowledged as primary decomposers, but the keystone taxa within the bacterial community regulating C loss from cultivated peatlands remain largely unknown. In this study, we investigated the bacterial taxa driving peat C mineralization during rice cultivation. Cultivation significantly decreased concentrations of soil organic C, dissolved organic C (DOC), carbohydrates, and phenolics but increased C mineralization rate (CMR). Consistent with the classic theory that phenolic inhibition creates a "latch" that reduces peat C decomposition, phenolics were highly negatively correlated with CMR in cultivated peatlands, indicating that elimination of inhibitory phenolics can accelerate soil C mineralization. Bacterial communities were significantly different following peatland cultivation, and co-occurrence diagnosis analysis revealed substantial changes in network clusters of closely connected nodes (modules) and bacterial keystone taxa. Specifically, in cultivated peatlands, bacterial modules were significantly negatively correlated with phenolics, carbohydrates, and DOC. While keystone taxa , , and can regulate bacterial modules and promote carbon mineralization. Those observations indicated that changes in bacterial modules can promote phenolic decomposition and eliminate phenolic inhibition of labile C decomposition, thus accelerating soil organic C loss during rice cultivation. Overall, the study provides deeper insights into microbe-driven peat C loss during rice cultivation and highlights the crucial role of keystone bacterial taxa in the removal of phenolic constraints on peat C preservation.
PubMed: 38500699
DOI: 10.1093/ismeco/ycae022 -
Journal, Genetic Engineering &... Mar 2024Choline oxidase, a flavoprotein, is an enzyme that catalyzes the reaction which converts choline into glycine betaine. Choline oxidase started its journey way back in...
BACKGROUND
Choline oxidase, a flavoprotein, is an enzyme that catalyzes the reaction which converts choline into glycine betaine. Choline oxidase started its journey way back in 1933. However, the impact of the high temperature on its structure has not been explored despite the long history and availability of its crystal structure. Both choline oxidase and its product, glycine betaine, have enormous applications spanning across multiple industries. Understanding how the 3D structure of the enzyme will change with the temperature change can open new ways to make it more stable and useful for industry.
PROCESS
This research paper presents the in-silico study and analysis of the structural changes of A. globiformis choline oxidase at temperatures from 25 °C to 60 °C. A step-wise process is depicted in Fig. 1.
RESULTS
Multiple sequence alignment (MSA) of 11 choline oxidase sequences from different bacteria vs Arthrobacter globiformis choline oxidase showed that active site residues are highly conserved. The available crystal structure of A. globiformis choline oxidase with cofactor Flavin Adenine Dinucleotide (FAD) in the dimeric state (PDB ID: 4MJW) was considered for molecular dynamics simulations. A simulated annealing option was used to gradually increase the temperature of the system from 25 °C to 60 °C. Analysis of the conserved residues, as well as residues involved in Flavin Adenine Dinucleotide (FAD) binding, substrate binding, substate gating, and dimer formationwas done. At high temperatures, the formation of the inter-chain salt bridge between Arg50 and Glu63 was a significant observation near the active site of choline oxidase.
CONCLUSION
Molecular dynamics studies suggest that an increase in temperature has a significant impact on the extended Flavin Adenine Dinucleotide (FAD) binding region. These changes interfere with the entry of substrate to the active site of the enzyme and make the enzyme inactive.
PubMed: 38494262
DOI: 10.1016/j.jgeb.2023.100348