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Chemical pesticides have an immense role in curbing the infection of plant viruses and soil-borne pathogens of high valued crops. However, the usage of chemical pesticides also contributes to the development of resistance among pathogens. Hence, attempts were made in this study to identify a suitable bacterial antagonist for managing viral and fungal pathogens infecting crop plants. Based on our earlier investigations, we identified Bacillus amyloliquefaciens VB7 as a potential antagonist for managing Sclerotinia sclerotiorum infecting carnation, tobacco streak virus infecting cotton and groundnut bud necrosis infecting tomato. Considering the multifaceted action of B. amyloliquefaciens VB7, attempts were made for whole-genome sequencing to assess the antiviral activity against tomato spotted wilt virus infecting chrysanthemum and antifungal action against Fusarium oxysporum f. sp. cubense (Foc). Genome annotation of the isolate B. amyloliquefaciens VB7 was confirmed as B. velezensis VB7 with accession number CP047587. Genome analysis revealed the presence of 9,231,928 reads with an average read length of 149 bp. Assembled genome had 1 contig, with a total length of 3,021,183 bp and an average G+C content of 46.79%. The protein-coding sequences (CDS) in the genome was 3090, transfer RNA (tRNA) genes were 85 with 29 ribosomal RNA (rRNA) genes and 21 repeat regions. The genome of B. velezensis VB7 had 506 hypothetical proteins and 2584 proteins with functional assignments. VB7 genome had the presence of flagellin protein FlaA with 987 nucleotides and translation elongation factor TU (Ef-Tu) with 1191 nucleotides. The identified ORFs were 3911 with 47.22% GC content. Non ribosomal pepide synthetase cluster (NRPS) gene clusters in the genome of VB7, coded for the anti-microbial peptides surfactin, butirosin A/butirosin B, fengycin, difficidin, bacillibactin, bacilysin, and mersacidin the Ripp lanthipeptide. Antiviral action of VB7 was confirmed by suppression of local lesion formation of TSWV in the local lesion host cowpea (Co-7). Moreover, combined application of B. velezensis VB7 with phyto-antiviral principles M. Jalapa and H. cupanioides increased shoot length, shoot diameter, number of flower buds per plant, flower diameter, and fresh weight of chrysanthemum. Further, screening for antifungal action of VB7 expressed antifungal action against Foc in vitro by producing VOC/NVOC compounds, including hexadecanoic acid, linoelaidic acid, octadecanoic acid, clindamycin, formic acid, succinamide, furanone, 4H-pyran, nonanol and oleic acid, contributing to the total suppression of Foc apart from the presence of NRPS gene clusters. Thus, our study confirmed the scope for exploring B. velezensis VB7 on a commercial scale to manage tomato spotted wilt virus, groundnut bud necrosis virus, tobacco streak virus, S. sclerotiorum, and Foc causing panama wilt of banana.

The animal gut has a remarkable abundance of microbes. These microbes have strong potential for biosynthesis of promising drug candidates, and these small bioactive molecules often medicate important host-microbe and microbe-microbe interactions. To understand the evolution of the animal gut microbes and their biosynthetic gene clusters, we characterized 24 faecal samples from different herbivores, carnivores and omnivores, by next-generation sequencing of the 16S rDNA V3-V4 hypervariable regions and NRPS. The results showed that the host diet and phylogeny both not only influence the bacterial communities, but also that NRPS gene clusters co-diversified with their gut microbiota. We also found that the animal gut microbiome contains abundant secondary metabolic synthesis gene clusters, which prove to be a potential gold mine of novel bioactive natural products. In conclusion, our results reveal the co-diversity of animal gut microbiota and their NRPS gene clusters, and suggest that potential NRPS natural products are hidden in the animal microbiome.

To evaluate the adsorption mechanism and performance of phosphate onto the composite of low-cost biochar and iron oxide, four biochar–iron oxides, namely biochar–magnetite (BC-M), biochar–ferrihydrite (BC-F), biochar–goethite (BC-G), and biochar–hematite (BC-H), were prepared by fabricating iron oxide to porous biochar. The biochar–iron oxides had huge surface areas of 691–864 m 2 /g and average pore diameters of 3.4–4.0 nm. Based on the characterization analysis of FTIR, XRD, XPS, and zeta potential, the interactions of electrostatic attraction, ligand exchange, and deposition dominated the phosphate adsorption onto biochar–iron oxides. The maximum adsorption capacity of phosphate followed the order of BC-G > BC-F > BC-H > BC-M. The isotherm data of BC-M and BC-H were well fitted by the Langmuir and Freundlich models, while those of BC-G and BC-F followed the Langmuir model. In addition, BC-M, BC-F, BC-G, and BC-H owned excellent regeneration ability and adsorption performance in practical (simulated) wastewater environment. Then the biochar–iron oxides exerted extensive and satisfactory prospect in wastewater remediation and recycling application in soil.

Marine sponge-associated microorganisms have proven to be a very promising source of biologically active and pharmaceutically important natural products. In this study, we investigated the diversity and antibacterial potential of bacteria from 49 sponge species isolated from the Beibu Gulf, South China Sea, belonging to 16 genera and several unidentified taxa. Using a variety of selective media, 363 strains with different morphologies were identified to six bacterial taxa, including Proteobacteria (α-subgroup 85 and γ-subgroup 59), Actinobacteria (123), Firmicutes (90), Bacteroidetes (5) and Brevundimonas (1). Media ISP2 and R2A were the most effective for isolating Actinobacteria. One hundred and twenty-three actinobacterial strains clustered into 21 genera identified by 16S rDNA gene sequencing, most of which were from the genus Microbacterium, followed by Pseudonocardia, Streptomyces, Kocuria, Aeromicrobium, Brachybacterium and Nocardiopsis, constituted 82% of total actinobacterial isolates. By using the minimal medium, 92 actinobacterial isolates showed antimicrobial activities, and 51 strains displayed moderate to strong antimicrobial activity that inhibited the growth of more than half of the bacteria tested in this study. Functional genes related to secondary metabolites were screened, revealing that 10% (12/123) of actinobacterial isolates contained PKS-KS genes, 18% (22/123) harbored NRPS-A genes and 6% (7/123) had hybrid PKS-NRPS gene clusters. The sponges Haliclona sp., Callyspongia sp. and Desmacella sp., belonging to class Demonspongiae, and Leucaltis sp. from the class Calcarea, were dominant hosts, harboring the most diverse actinobacterial genera with stronger antimicrobial activities and more diverse PKS/NRPS genes.

Background Phomafungin is a recently reported broad spectrum antifungal compound but its biosynthetic pathway is unknown. We combed publicly available Phoma genomes but failed to find any putative biosynthetic gene cluster that could account for its biosynthesis. Results Therefore, we sequenced the genome of one of our Phoma strains (F3723) previously identified as having antifungal activity in a high-throughput screen. We found a biosynthetic gene cluster that was predicted to synthesize a cyclic lipodepsipeptide that differs in the amino acid composition compared to Phomafungin. Antifungal activity guided isolation yielded a new compound, BII-Rafflesfungin, the structure of which was determined. Conclusions We describe the NRPS-t1PKS cluster ‘ BIIRfg’ compatible with the synthesis of the cyclic lipodepsipeptide BII-Rafflesfungin [HMHDA-L-Ala-L-Glu-L-Asn-L-Ser-L-Ser-D-Ser-D-allo-Thr-Gly]. We report new Stachelhaus codes for Ala, Glu, Asn, Ser, Thr, and Gly. We propose a mechanism for BII-Rafflesfungin biosynthesis, which involves the formation of the lipid part by BIIRfg_PKS followed by activation and transfer of the lipid chain by a predicted AMP-ligase on to the first PCP domain of the BIIRfg_NRPS gene.

Actinomycetes are known as a group of antimicrobial-producing bacteria. This is supported by the presence of potential genes in actinomycetes bacteria. These genes include Polyketide Synthase (PKS) and Non-Ribosomal Peptide Synthetase (NRPS). Detection of these genes using PCR requires the optimum annealing temperature so that the detection process runs accurately. The purpose of this study was to determine the appropriate annealing temperature in the detection of PKS I, PKS II and NRPS genes in actinomycetes bacterial isolates. The study was carried out experimentally with varying annealing temperatures of 52°C and 55°C. The results showed that all three genes were detected at 52°C, while at 55°C the PKS I gene bands were faint, and no PKS II and NRPS gene bands were found. Based on the results obtained, a temperature of 52°C is a suitable temperature for the detection of PKS I, II and NRPS genes.

Tetrodotoxins (TTXs), potent neurotoxins, have become an increasing concern in Europe in recent decades, especially because of their presence in mollusks. The European Food Safety Authority published a Scientific Opinion setting a recommended threshold for TTX in mollusks of 44 µg equivalent kg−1 and calling all member states to contribute to an effort to gather data in order to produce a more exhaustive risk assessment. The objective of this work was to assess TTX levels in wild and farmed mussels (Mytilus galloprovincialis) harvested in 2018–2019 along the coastal area of the Marche region in the Central Adriatic Sea (Italy). The presence of Vibrio spp. carrying the non-ribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) genes, which are suspected to be involved in TTX biosynthesis, was also investigated. Out of 158 mussel samples analyzed by hydrophilic interaction liquid chromatography coupled with tandem mass spectrometry (HILIC-MS/MS), 11 (7%) contained the toxins at detectable levels (8–26 µg kg−1) and 3 (2%) contained levels above the EFSA safety threshold (61–76 µg kg−1). Contaminated mussels were all harvested from natural beds in spring or summer. Of the 2019 samples, 70% of them contained V. alginolyticus strains with the NRPS and/or PKS genes. None of the strains containing NRPS and/or PKS genes showed detectable levels of TTXs. TTXs in mussels are not yet a threat in the Marche region nor in Europe, but further investigations are surely needed.

Basal stem rot (BSR) of oil palm is a disastrous disease caused by a white-rot fungus Ganoderma boninense Pat. Non-ribosomal peptides (NRPs) synthesized by non-ribosomal peptide synthetases (NRPSs) are a group of secondary metabolites that act as fungal virulent factors during pathogenesis in the host. In this study, we aimed to isolate NRPS gene of G. boninense strain UPMGB001 and investigate the role of this gene during G. boninense -oil palm interaction. The isolated NRPS DNA fragment of 8322 bp was used to predict the putative peptide sequence of different domains and showed similarity with G. sinense (85%) at conserved motifs of three main NRPS domains. Phylogenetic analysis of NRPS peptide sequences demonstrated that NRPS of G. boninense belongs to the type VI siderophore family. The roots of 6-month-old oil palm seedlings were artificially inoculated for studying NRPS gene expression and disease severity in the greenhouse. The correlation between high disease severity (50%) and high expression (67-fold) of G. boninense NRPS gene at 4 months after inoculation and above indicated that this gene played a significant role in the advancement of BSR disease. Overall, these findings increase our knowledge on the gene structure of NRPS in G. boninense and its involvement in BSR pathogenesis as an effector gene.

Streptococcus mutans is a major pathogen causing human dental caries. As a Gram-positive bacterium with a small genome (about 2 Mb) it is considered a poor source of natural products. Due to a recent explosion in genomic data available for S. mutans strains, we were motivated to explore the natural product production potential of this organism. Bioinformatic characterization of 169 publically available genomes of S. mutans from human dental caries revealed a surprisingly rich source of natural product biosynthetic gene clusters. Anti-SMASH analysis identified one nonribosomal peptide synthetase (NRPS) gene cluster, seven polyketide synthase (PKS) gene clusters and 136 hybrid PKS/NRPS gene clusters. In addition, 211 ribosomally synthesized and post-translationally modified peptides (RiPPs) clusters and 615 bacteriocin precursors were identified by a combined analysis using BAGEL and anti-SMASH. S. mutans harbors a rich and diverse natural product genetic capacity, which underscores the importance of probing the human microbiome and revisiting species that have traditionally been overlooked as “poor” sources of natural products.

Bacteria from the genus Paenibacillus make a variety of antimicrobial compounds, including lipopeptides produced by a non-ribosomal synthesis mechanism (NRPS). In the present study, we show the genomic and phenotypical characterization of Paenibacillus elgii AC13 which makes three groups of small molecules: the antimicrobial pelgipeptins and two other families of peptides that have not been described in P. elgii. A family of lipopeptides with [M + H]+ 1664, 1678, 1702, and 1717 m/z was purified from the culture cell fraction. Partial characterization revealed that they are similar to tridecaptin from P. terrae. However, they present amino acid chain modifications in positions 3, 7, and 10. These new variants were named tridecaptin G1, G2, G3, and G4. Furthermore, a gene cluster was identified in P. elgii AC13 genome, revealing high similarity to the tridecaptin-NRPS gene cluster from P. terrae. Tridecaptin G1 and G2 showed in vitro antimicrobial activity against Escherichia coli, Klebsiella pneumonia (including a multidrug-resistant strain), Staphylococcus aureus, and Candida albicans. Tri G3 did not show antimicrobial activity against S. aureus and C. albicans at all tested concentrations. An intriguing feature of this family of lipopeptides is that it was only observed in the cell fraction of the P. elgii AC13 culture, which could be a result of the amino acid sequence modifications presented in these variants.