Paenibacillus anseongense sp. nov. a Silver Nanoparticle Producing Bacterium Isolated from Rhizospheric Soil

Paenibacillus hexagrammi sp. nov., a novel bacterium isolated from the gut content of Hexagrammos agrammus

A Gram-stain-positive, aerobic bacterium, designated as YPD9-1T, was isolated from the gut contents of a spotty belly greenling, Hexagrammos agrammus, collected near Dokdo island, South Korea. The rod-shaped cells were oxidase-positive, and catalase-negative. The major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, C16 : 0, iso-C16 : 0 and iso-C17: 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and two unidentified lipids. The DNA G+C content was 47.6 mol% and the predominant respiratory quinone was menaquinone MK-7. The 16S rRNA gene sequence of YPD9-1T showed low sequence similarities to species of the genus Paenibacillus, Paenibacillus pocheonensis Gsoil 1138T (97.21 % of sequence similarity), Paenibacillus aestuarii CJ25T (97.12 %) and Paenibacillus allorhizoplanae JJ-42T (96.89 %). The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that YPD9-1T formed a distinct branch among other species of the genus Paenibacillus. The digital DNA-DNA hybridisation, average nucleotide identity, and average amino acid identity values between YPD9-1T and the related species were in the ranges of 15.3-16.2 %, 74.1-78.4 %, and 71.1-71.9 %, respectively, which are below the species cutoff values. On the basis of the results of the polyphasic analysis, we conclude that strain YPD9-1T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus hexagrammi sp. nov. is proposed. The type strain of Paenibacillus hexagrammi is YPD9-1T (=KCTC 43424T =LMG 32988T).

Optimization of the biosynthesis of silver nanoparticles using bacterial extracts and their antimicrobial potential

In the present study, silver nanoparticles (AgNPs) were biosynthesized using the supernatant and the intracellular extract of Cupriavidus necator, Bacillus megaterium, and Bacillus subtilis. The characterization of the AgNPs was carried out using UV-Vis spectroscopy, FTIR, DLS and TEM. Resazurin microtiter-plate assay was used to determine the antimicrobial action of AgNPs against Escherichia coli. UV-Visible spectra showed peaks between 414 and 460 nm. TEM analysis revealed that the synthesized AgNPs showed mostly spherical shapes. DLS results determined sizes from 20.8 to 118.4 nm. The highest antimicrobial activity was obtained with the AgNPs synthesized with supernatant rather than those using the intracellular extract. Therefore, it was determined that the bacterial species, temperature, pH, and type of extract (supernatant or intracellular) influence the biosynthesis. This synthesis thus offers a simple, environmentally friendly, and low-cost method for the production of AgNPs, which can be used as antibacterial agents.

Characterization and in-depth genome analysis of a halotolerant probiotic bacterium Paenibacillus sp. S-12, a multifarious bacterium isolated from Rauvolfia serpentina

BACKGROUND

Members of Paenibacillus genus from diverse habitats have attracted great attention due to their multifarious properties. Considering that members of this genus are mostly free-living in soil, we characterized the genome of a halotolerant environmental isolate belonging to the genus Paenibacillus. The genome mining unravelled the presence of CAZymes, probiotic, and stress-protected genes that suggested strain S-12 for industrial and agricultural purposes.

RESULTS

Molecular identification by 16 S rRNA gene sequencing showed its closest match to other Paenibacillus species. The complete genome size of S-12 was 5.69 Mb, with a GC-content 46.5%. The genome analysis of S-12 unravelled the presence of an open reading frame (ORF) encoding the functions related to environmental stress tolerance, adhesion processes, multidrug efflux systems, and heavy metal resistance. Genome annotation identified the various genes for chemotaxis, flagellar motility, and biofilm production, illustrating its strong colonization ability.

CONCLUSION

The current findings provides the in-depth investigation of a probiotic Paenibacillus bacterium that possessed various genome features that enable the bacterium to survive under diverse conditions. The strain shows the strong ability for probiotic application purposes.

Silver Nanoparticles of Artemisia sieberi Extracts: Chemical Composition and Antimicrobial Activities

BACKGROUND

Artemisia sieberi (mugwort) is a member of the daisy family Asteraceae and is widely propagated in Saudi Arabia. A. sieberi has historical medical importance in traditional societies. The current study aimed to assess the antibacterial and antifungal characteristics of the aqueous and ethanolic extracts of A. sieberi. In addition, the study investigated the effect of silver nanoparticles (AgNPs) synthesized from the A. sieberi extract.

METHODS

The ethanolic and aqueous extracts and AgNPs were prepared from the shoots of A. sieberi. The characteristics of AgNPs were assessed by UV-visible spectroscopy, transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FTIR), and dynamic light scattering (DLS). The antibacterial experiments were performed against Staphylococcus aureus, Bacillus subtilis, Escherichia coli, and Pseudomonas aeruginosa. The fungal species used were Candida parapsilosis, Candida krusei, Candida famata, Candida rhodotorula, and Candida albicans. The antibacterial and antifungal characteristics were evaluated by measuring the diameter of growing organisms in Petri dishes treated with different concentrations of either extracts or AgNPs compared to the untreated controls. Furthermore, TEM imaging was used to investigate any ultrastructure changes in the microbes treated with crude extracts and AgNO₃.

RESULTS

The ethanolic and aqueous extracts significantly decreased the growth of E. coli, S. aureus, and B. subtilis (p < 0.001), while P. aeruginosa was not affected. Unlike crude extracts, AgNPs had more substantial antibacterial effects against all species. In addition, the mycelial growth of C. famata was reduced by the treatment of both extracts. C. krusei mycelial growth was decreased by the aqueous extract, while the growth of C. parapsilosis was affected by the ethanolic extract and AgNPs (p < 0.001). None of the treatments affected the growth of C. albicans or C. rhodotorula. TEM analysis showed cellular ultrastructure changes in the treated S. aureus and C. famata compared to the control.

CONCLUSION

The biosynthesized AgNPs and extracts of A. sieberi have a potential antimicrobial characteristic against pathogenic bacterial and fungal strains and nullified resistance behavior.

Acid protease functionalized novel silver nanoparticles (APTs-AgNPs): A new approach towards photocatalytic and biological applications

Herein, we described for the first time, an efficient biogenic synthesis of APTs-AgNPs using acid protease from Melilotus indicus leaf extract. The acid protease (APTs) has an essential role in the stabilization, reduction, and capping of APTs-AgNPs. The crystalline nature, size, and surface morphology of APTs-AgNPs were examined using different techniques such as XRD, UV, FTIR, SEM, EDS, HRTEM, and DLS analysis. The generated APTs-AgNPs demonstrated notable performance as dual functionality (photocatalyst and antibacterial disinfection). By destroying 91 % of methylene blue (MB) in <90 min of exposure, APTs-AgNPs demonstrated remarkable photocatalytic activity. APTs-AgNPs also showed remarkable stability as a photocatalyst after five test cycles. Furthermore, the APTs-AgNPs was found to be a potent antibacterial agent with inhibition zones of 30(±0.5 mm), 27(±0.4 mm), 16(±0.1 mm), and 19(±0.7 mm) against Gram-positive (Staphylococcus aureus) and Gram-negative (Escherichia coli) bacteria, respectively, under both light and dark conditions. Furthermore, APTs-AgNPs effectively scavenged 2,2-diphenyl-1-picrylhydrazyl (DPPH) radicals, demonstrating their potent antioxidant activity. The outcomes of this study thus demonstrates the dual functionality of APTs-AgNPs produced using the biogenic approach method as a photocatalyst and an antibacterial agent for effective microbial and environmental control.

Paenibacillus alkalitolerans sp. nov., a bacterium isolated from a salt lake of Turpan City in Xinjiang Province, north-west China

A Gram stain-positive, rod-shaped, motile, aerobic and terminal endospore formation bacterium, designated YIM B00362^T, was isolated from saline soil samples collected from a salt lake in Xinjiang Province, north-west China. Phylogenetic analysis based on the 16S rRNA gene sequences and whole genomes indicated that the isolate belongs to the genus Paenibacillus. However, the highest sequence similarity between strain YIM B00362^T and the relatives was only 94.4%. Moreover, the DNA-DNA relatedness and ANI values between the novel isolate and the relative type strain, Paenibacillus antri SYSU K30003^T was 13.6% and 70.3%, respectively. The major cellular fatty acids were anteiso-C_15:0, C_16:0 and the major quinone was MK-7. The isolate contained meso-diaminopimelic acid as the diagnostic diamino acid and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylglyceride, and two unidentified polar lipids. The genomic DNA G + C content was 50.9 mol%. The major whole-cell sugars contained glucose and galactose. On the basis of physiological, phenotypic, and chemotaxonomic data, strain YIM B00362^T represents a novel species of genus Paenibacillus, for which the name Paenibacillus alkalitolerans sp. nov. is proposed. The type strain is YIM B00362^T (= KCTC 43272 ^T = CGMCC 1.18801 ^T = NBRC 114667 ^T).

Paenibacillus vietnamensis sp. nov., isolated from the rhizosphere soil of Arachis hypogaea

A novel bacterial strain, N4T, was isolated from the soil of a groundnut Arachis hypogaea field in Nghean province, Vietnam. The phylogenetic, chemotaxonomic and phenotypic characteristics of this strain were determined. Cells of strain N4T were Gram-negative, aerobic, endospore-forming and rod-shaped. Strain N4T grew at 20–37 °C (optimum, 30 °C), pH 6–10 (optimum, pH 7) and 0–5 % NaCl (optimum, 0 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain N4T belonged to the genus Paenibacillus and was closely related to Paenibacillus harenae B519T (=KCTC 3951T) and Paenibacillus alkaliterrae KSL-134T (=KCTC 3956T) with 96.3 and 96.5% gene sequence similarity, respectively. It contained meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. The DNA G+C content was 52.9 mol%. The major isoprenoid quinone was MK-7. Anteiso-C15 : 0 and iso-C16 : 0 were the dominant cellular fatty acids. Based on phylogenetic, physiological and biochemical characteristics, strain N4T represents a novel species of the genus Paenibacillus , for which the name Paenibacillus vietnamensis sp. nov. is proposed. The type strain is N4T (=KCTC 33932T= VTCC 12236T).

Genome mining reveals polysaccharide-degrading potential and new antimicrobial gene clusters of novel intestinal bacterium Paenibacillus jilinensis sp. nov

Background

Drug-resistant bacteria have posed a great threat to animal breeding and human health. It is obviously urgent to develop new antibiotics that can effectively combat drug-resistant bacteria. The commensal flora inhabited in the intestines become potential candidates owing to the production of a wide range of antimicrobial substances. In addition, host genomes do not encode most of the enzymes needed to degrade dietary structural polysaccharides. The decomposition of these polysaccharides mainly depends on gut commensal-derived CAZymes.

Results

We report a novel species isolated from the chicken intestine, designated as Paenibacillus jilinensis sp. nov. and with YPG26^T (= CCTCC M2020899^T) as the type strain. The complete genome of P. jilinensis YPG26^T is made up of a single circular chromosome measuring 3.97 Mb in length and containing 49.34% (mol%) G + C. It carries 33 rRNA genes, 89 tRNA genes, and 3871 protein-coding genes, among which abundant carbohydrate-degrading enzymes (CAZymes) are encoded. Moreover, this strain has the capability to antagonize multiple pathogens in vitro. We identified putative 6 BGCs encoding bacteriocin, NRPs, PKs, terpenes, and protcusin by genome mining. In addition, antibiotic susceptibility testing showed sensitivity to all antibiotics tested.

Conclusions

This study highlights the varieties of CAZymes genes and BGCs in the genome of Paenibacillus jilinensis. These findings confirm the beneficial function of the gut microbiota and also provide a promising candidate for the development of new carbohydrate degrading enzymes and antibacterial agents.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08623-4.

Green Synthesis and Potential Antibacterial Applications of Bioactive Silver Nanoparticles: A Review

Green synthesis of silver nanoparticles (AgNPs) using biological resources is the most facile, economical, rapid, and environmentally friendly method that mitigates the drawbacks of chemical and physical methods. Various biological resources such as plants and their different parts, bacteria, fungi, algae, etc. could be utilized for the green synthesis of bioactive AgNPs. In recent years, several green approaches for non-toxic, rapid, and facile synthesis of AgNPs using biological resources have been reported. Plant extract contains various biomolecules, including flavonoids, terpenoids, alkaloids, phenolic compounds, and vitamins that act as reducing and capping agents during the biosynthesis process. Similarly, microorganisms produce different primary and secondary metabolites that play a crucial role as reducing and capping agents during synthesis. Biosynthesized AgNPs have gained significant attention from the researchers because of their potential applications in different fields of biomedical science. The widest application of AgNPs is their bactericidal activity. Due to the emergence of multidrug-resistant microorganisms, researchers are exploring the therapeutic abilities of AgNPs as potential antibacterial agents. Already, various reports have suggested that biosynthesized AgNPs have exhibited significant antibacterial action against numerous human pathogens. Because of their small size and large surface area, AgNPs have the ability to easily penetrate bacterial cell walls, damage cell membranes, produce reactive oxygen species, and interfere with DNA replication as well as protein synthesis, and result in cell death. This paper provides an overview of the green, facile, and rapid synthesis of AgNPs using biological resources and antibacterial use of biosynthesized AgNPs, highlighting their antibacterial mechanisms.

Pinibacter aurantiacus gen. nov., sp. nov., isolated from rhizospheric soil of a pine tree

A Gram-stain-negative, aerobic and rod-shaped novel bacterial strain, designated MAH-26^T, was isolated from rhizospheric soil of a pine tree. The colonies were orange coloured, smooth, spherical and 0.7-1.8 mm in diameter when grown on Reasoner's 2A (R2A) agar for 2 days. Strain MAH-26^T was able to grow at 10-40 °C, at pH 6.0-9.0 and with 0-1.0 % NaCl. Cell growth occurred on nutrient agar, R2A agar, tryptone soya agar and Luria-Bertani agar. The strain gave positive results in oxidase and catalase tests. Strain MAH-26^T was closely related to Flavihumibacter sediminis CJ663^T and Parasegetibacter terrae SGM2-10^T with a low 16S rRNA gene sequence similarity (92.8 and 92.9 %, respectively) and phylogenetic analysis indicated that the strain formed a distinct phylogenetic lineage from the members of the closely related genera of the family Chitinophagaceae. Strain MAH-26^T has a draft genome size of 6 857 405 bp, annotated with 5173 protein-coding genes, 50 tRNA and two rRNA genes. The genomic DNA G+C content was 41.5 mol%. The predominant isoprenoid quinone was menaquinone 7. The major fatty acids were identified as iso-C_15:0, iso-C_15:1 G and iso-C_17:0 3OH. On the basis of phylogenetic inference and phenotypic, chemotaxonomic and molecular properties, strain MAH-26^T represents a novel species of a novel genus of the family Chitinophagaceae, for which the name Pinibacter aurantiacus gen. nov., sp. nov. is proposed. The type strain of Pinibacter aurantiacus is MAH-26^T (=KACC 19749^T=CGMCC 1.13701^T).

Characterization and Genome Analysis of Arthrobacter bangladeshi sp. nov., Applied for the Green Synthesis of Silver Nanoparticles and Their Antibacterial Efficacy against Drug-Resistant Human Pathogens

The present study describes the isolation and characterization of novel bacterial species Arthrobacter bangladeshi sp. nov., applied for the green synthesis of AgNPs, and investigates its antibacterial efficacy against drug-resistant pathogenic Salmonella Typhimurium and Yersinia enterocolitica. Novel strain MAHUQ-56T is Gram-positive, aerobic, non-motile, and rod-shaped. Colonies were spherical and milky white. The strain showed positive activity for catalase and nitrate reductase, and the hydrolysis of starch, L-tyrosine, casein, and Tween 20. On the basis of the 16S rRNA gene sequence, strain MAHUQ-56T belongs to the Arthrobacter genus and is most closely related to Arthrobacter pokkalii P3B162T (98.6%). Arthrobacter bangladeshi MAHUQ-56T has a genome 4,566,112 bp long (26 contigs) with 4125 protein-coding genes, 51 tRNA and 6 rRNA genes. The culture supernatant of Arthrobacter bangladeshi MAHUQ-56T was used for the easy and green synthesis of AgNPs. Synthesized AgNPs were characterized by UV-vis spectroscopy, FE-TEM, XRD, DLS, and FT-IR. Synthesized AgNPs were spherical and 12-50 nm in size. FT-IR analysis revealed various biomolecules that may be involved in the synthesis process. Synthesized AgNPs showed strong antibacterial activity against multidrug-resistant pathogenic S. typhimurium and Y. enterocolitica. MIC values of the synthesized AgNPs against S. typhimurium and Y. enterocolitica were 6.2 and 3.1 ug/mL, respectively. The MBC of synthesized AgNPs for both pathogens was 12.5 ug/mL. FE-SEM analysis revealed the morphological and structural alterations, and damage of pathogens treated by AgNPs. These changes might disturb normal cellular functions, which ultimately leads to the death of cells.

Biosynthesis, Characterization and Antibacterial Application of Novel Silver Nanoparticles against Drug Resistant Pathogenic Klebsiella pneumoniae and Salmonella Enteritidis

The present study highlights the biosynthesis of silver nanoparticles (AgNPs) using culture supernatant of Massilia sp. MAHUQ-52 as well as the antimicrobial application of synthesized AgNPs against multi-drug resistant pathogenic Klebsiella pneumoniae and Salmonella Enteritidis. Well-defined AgNPs formation occurred from the reaction mixture of cell-free supernatant and silver nitrate (AgNO3) solution within 48 h of incubation. UV-visible spectroscopy analysis showed a strong peak at 435 nm, which corresponds to the surface plasmon resonance of AgNPs. The synthesized AgNPs were characterized by FE-TEM, EDX, XRD, DLS and FT-IR. From FE-TEM analysis, it was found that most of the particles were spherical shape, and the size of synthesized nanoparticles (NPs) was 15-55 nm. EDX spectrum revealed a strong silver signal at 3 keV. XRD analysis determined the crystalline, pure, face-centered cubic AgNPs. FT-IR analysis identified various functional molecules that may be involved with the synthesis and stabilization of AgNPs. The antimicrobial activity of Massilia sp. MAHUQ-52 mediated synthesized AgNPs was determined using the disk diffusion method against K. pneumoniae and S. Enteritidis. Biosynthesized AgNPs showed strong antimicrobial activity against both K. pneumoniae and S. Enteritidis. The MICs of synthesized AgNPs against K. pneumoniae and S. Enteritidis were 12.5 and 25.0 μg/mL, respectively. The MBC of biosynthesized AgNPs against both pathogens was 50.0 μg/mL. From FE-SEM analysis, it was found that the AgNPs-treated cells showed morphological changes with irregular and damaged cell walls that culminated in cell death.

Bacterial Mediated Rapid and Facile Synthesis of Silver Nanoparticles and Their Antimicrobial Efficacy against Pathogenic Microorganisms

In the present study, silver nanoparticles (AgNPs), biosynthesized using culture supernatant of bacterial strain Paenarthrobacter nicotinovorans MAHUQ-43, were characterized and their antimicrobial activity was investigated against both Gram-positive Bacillus cereus and Gram-negative bacteria Pseudomonas aeruginosa. Bacterial-mediated synthesized AgNPs were characterized by UV-Visible (UV-Vis) spectrophotometer, field emission-transmission electron microscopy (FE-TEM), energy dispersive X-ray (EDX), X-ray diffraction (XRD), Fourier transform infrared (FTIR) spectroscopy, and dynamic light scattering (DLS) analysis. The UV-Vis spectral analysis showed the absorption maxima at 466 nm which assured the synthesis of AgNPs. The FE-TEM analysis revealed the spherical shape of nanoparticles with the size range from 13 to 27 nm. The EDX and XRD analysis ensured the crystalline nature of biosynthesized AgNPs. The FTIR analysis revealed the involvement of different biomolecules for the synthesis of AgNPs as reducing and capping agents. The bacterial-mediated synthesized AgNPs inhibited the growth of pathogenic strains B. cereus and P. aeruginosa and developed a clear zone of inhibition (ZOI). The MIC and MBC for both pathogens were 12.5 µg/mL and 25 µg/mL, respectively. Moreover, field emission scanning electron microscopy analysis revealed that the synthesized AgNPs can destroy the outer membrane and alter the cell morphology of treated pathogens, leading to the death of cells. This study concludes the eco-friendly, facile and rapid synthesis of AgNPs using P. nicotinovorans MAHUQ-43 and synthesized AgNPs showed excellent antimicrobial activity against both Gram-positive and Gram-negative pathogens.

The Reaction of Cellulolytic and Potentially Cellulolytic Spore-Forming Bacteria to Various Types of Crop Management and Farmyard Manure Fertilization in Bulk Soil

The ecology of cellulolytic bacteria in bulk soil is still relatively unknown. There is still only a handful of papers on the abundance and diversity of this group of bacteria. Our study aimed to determine the impact of various crop management systems and farmyard manure (FYM) fertilization on the abundance of cellulolytic and potentially cellulolytic spore-forming bacteria (SCB). The study site was a nearly 100-year-old fertilization experiment, one of the oldest still active field trials in Europe. The highest contents of total carbon (TC) and total nitrogen (TN) were recorded in both five-year rotations. The abundances of SCB and potential SCB were evaluated using classical microbiological methods, the most probable number (MPN), and 16S rRNA Illumina MiSeq sequencing. The highest MPN of SCB was recorded in soil with arbitrary rotation without legumes (ARP) fertilized with FYM (382 colony-forming units (CFU) mL−1). As a result of the bioinformatic analysis, the highest values of the Shannon–Wiener index and the largest number of operational taxonomic units (OTUs) were found in ARP-FYM, while the lowest in ARP treatment without FYM fertilization. In all treatments, those dominant at the order level were: Brevibacillales (13.1–43.4%), Paenibacillales (5.3–36.9%), Bacillales (4.0–0.9%). Brevibacillaceae (13.1–43.4%), Paenibacillaceae (8.2–36.9%), and Clostridiaceae (5.4–11.9%) dominated at the family level in all tested samples. Aneurinibacillaceae and Hungateiclostridiaceae families increased their overall share in FYM fertilization treatments. The results of our research show that the impact of crop management types on SCB was negligible while the actual factor shaping SCB community was the use of FYM fertilization.

Ecofriendly Synthesis of Silver Nanoparticles by Terrabacter humi sp. nov. and Their Antibacterial Application against Antibiotic-Resistant Pathogens

It is essential to develop and discover alternative eco-friendly antibacterial agents due to the emergence of multi-drug-resistant microorganisms. In this study, we isolated and characterized a novel bacterium named Terrabacter humi MAHUQ-38^T, utilized for the eco-friendly synthesis of silver nanoparticles (AgNPs) and the synthesized AgNPs were used to control multi-drug-resistant microorganisms. The novel strain was Gram stain positive, strictly aerobic, milky white colored, rod shaped and non-motile. The optimal growth temperature, pH and NaCl concentration were 30 °C, 6.5 and 0%, respectively. Based on 16S rRNA gene sequence, strain MAHUQ-38^T belongs to the genus Terrabacter and is most closely related to several Terrabacter type strains (98.2%-98.8%). Terrabacter humi MAHUQ-38^T had a genome of 5,156,829 bp long (19 contigs) with 4555 protein-coding genes, 48 tRNA and 5 rRNA genes. The culture supernatant of strain MAHUQ-38^T was used for the eco-friendly and facile synthesis of AgNPs. The transmission electron microscopy (TEM) image showed the spherical shape of AgNPs with a size of 6 to 24 nm, and the Fourier transform infrared (FTIR) analysis revealed the functional groups responsible for the synthesis of AgNPs. The synthesized AgNPs exhibited strong anti-bacterial activity against multi-drug-resistant pathogens, Escherichia coli and Pseudomonas aeruginosa. Minimal inhibitory/bactericidal concentrations against E. coli and P. aeruginosa were 6.25/50 and 12.5/50 μg/mL, respectively. The AgNPs altered the cell morphology and damaged the cell membrane of pathogens. This study encourages the use of Terrabacter humi for the ecofriendly synthesis of AgNPs to control multi-drug-resistant microorganisms.