3 Biotech最新文献

{"title":"PFusionDB: a comprehensive database of plant-specific fusion transcripts.","authors":"Ajay Arya, Simran Arora, Fiza Hamid, Shailesh Kumar","doi":"10.1007/s13205-024-04132-1","DOIUrl":"10.1007/s13205-024-04132-1","url":null,"abstract":"<p><p>Fusion transcripts (FTs) are well known cancer biomarkers, relatively understudied in plants. Here, we developed PFusionDB (www.nipgr.ac.in/PFusionDB), a novel plant-specific fusion-transcript database. It is a comprehensive repository of 80,170, 39,108, 83,330, and 11,500 unique fusions detected in 1280, 637, 697, and 181 RNA-Seq samples of <i>Arabidopsis thaliana</i>, <i>Oryza sativa japonica</i>, <i>Oryza sativa indica</i>, and <i>Cicer arietinum</i> respectively. Here, a total of 76,599 (<i>Arabidopsis thaliana</i>), 35,480 (<i>Oryza sativa japonica</i>), 72,099 (<i>Oryza sativa indica</i>), and 9524 (<i>Cicer arietinum</i>) fusion transcripts are non-recurrent i.e., only found in one sample. Identification of FTs was performed by using a total of five tools viz. EricScript-Plants, STAR-Fusion, TrinityFusion, SQUID, and MapSplice. At PFusionDB, available fundamental details of fusion events includes the information of parental genes, junction sequence, expression levels of fusion transcripts, breakpoint coordinates, strand information, tissue type, treatment information, fusion type, PFusionDB ID, and Sequence Read Archive (SRA) ID. Further, two search modules: 'Simple Search' and 'Advanced Search', along with a 'Browse' option to data download, are present for the ease of users. Three distinct modules viz. 'BLASTN', 'SW Align', and 'Mapping' are also available for efficient query sequence mapping and alignment to FTs. PFusionDB serves as a crucial resource for delving into the intricate world of fusion transcript in plants, providing researchers with a foundation for further exploration and analysis. Database URL: www.nipgr.ac.in/PFusionDB.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s13205-024-04132-1.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"14 11","pages":"282"},"PeriodicalIF":2.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11519250/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142542976","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":"Simultaneous detection of novel goose parvovirus and novel duck reovirus by SYBR Green I-based duplex real-time quantitative polymerase chain reaction.","authors":"Yimin Wang, Yong Wang, Zhuangli Bi, Yuhan Liu, Chunchun Meng, Jie Zhu, Guangqing Liu, Chuanfeng Li","doi":"10.1007/s13205-024-04139-8","DOIUrl":"10.1007/s13205-024-04139-8","url":null,"abstract":"<p><p>Co-infection with novel goose parvovirus (NGPV) and novel duck reovirus (NDRV) is common, significantly impeding duck growth and resulting in considerable economic losses within the duck farming industry. To facilitate rapid and accurate diagnosis and differentiation of these two viruses, this study developed a SYBR Green I-based duplex real-time quantitative polymerase chain reaction (qPCR) assay. This assay enabled the simultaneous detection of NGPV and NDRV by exploiting their distinct melting temperatures (Tm): 78.5 ± 0.50 °C for NGPV and 84.5 ± 0.50 °C for NDRV. No amplification was observed for other prevalent non-target duck viruses. The intra- and inter-assay coefficients of variation were less than 1.75%. The assay showed good performance with the same detection limit of 10² copies/μL for both NGPV and NDRV. The results of the clinical testing indicated that 45.3% (34/75) of the samples tested positive for NGPV, while 38.7% (29/75) were positive for NDRV. Notably, 13.3% (10/75) exhibited co-infection. These results revealed that the sensitivity of the developed method exceed that of conventional polymerase chain reaction (PCR). The developed method for the identifying of NGPV and NDRV shows good specificity, sensitivity, and repeatability, rendering it an effective tool for the simultaneous detection of co-infection with NGPV and NDRV.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"14 11","pages":"288"},"PeriodicalIF":2.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11532324/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142581853","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":"Composition and diversity of endophytic bacterial communities in the tubers of <i>Pinellia ternata</i> from different regions and their effects on succinate biosynthesis based on high-throughput sequencing.","authors":"Peng Zhang, Wei Ding, Heng Zheng","doi":"10.1007/s13205-024-04108-1","DOIUrl":"10.1007/s13205-024-04108-1","url":null,"abstract":"<p><p>In this study, high-throughput sequencing (HTS) technology was used to investigate the composition and diversity of endophytic bacteria and their effects on succinic acid biosynthesis in <i>P. ternata</i> tubers from three different geographical locations (MS, SL, and ZT). A total of 1777 amplicon sequence variants (ASVs) were annotated, and the diversity and composition of endophytic bacteria in <i>P. ternata</i> tubers were significantly different among different regions. The ZT samples presented the highest α diversity, and the Shannon diversity, richness, and Pielou evenness index were all ZT > MS > SL. Co-occurrence network analysis revealed that endophytic bacterial groups such as <i>Stenotrophomonas</i>, <i>Pseudomonas</i>, <i>Mycobacterium</i>, and <i>Chryseomicrobium</i> were key groups in the endophytic bacterial interaction network, indicating that they play a role in maintaining community stability. In addition, some endophytic bacteria were associated with the biosynthesis of succinic acid, a key bioactive compound in <i>P. ternata</i>. The succinate content was positively correlated with the genera <i>Brevundimonas</i>, <i>Ensifer</i>, <i>Nocardioides</i>, and <i>Paenibacillus</i>, while it was negatively correlated with the genera <i>Lentimicrobium</i>, <i>Anaerovorax</i>, and <i>Pajaroellobacter</i>. These findings highlight the key role of endophytic bacteria in regulating the efficacy of <i>P. ternata</i>. These findings provide key information for further elucidating the mechanism by which endophytic bacteria affect the synthesis of bioactive compounds.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"14 11","pages":"262"},"PeriodicalIF":2.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11456575/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142387131","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":"Cloning, heterologous expression and characterization of β-glucosidase deriving from <i>Moniliophthora perniciosa</i> (Stahel) Aime and Phillips Mora.","authors":"Alison Borges Vitor, Keilane Silva Farias, Geise Camila Araújo Ribeiro, Carlos Priminho Pirovani, Raquel Guimarães Benevides, Gonçalo Amarante Guimarães Pereira, Sandra Aparecida de Assis","doi":"10.1007/s13205-024-04128-x","DOIUrl":"10.1007/s13205-024-04128-x","url":null,"abstract":"<p><p>Β-glucosidase (BGLs) act synergistically with endoglucanases and exoglucanases and then are of great interest for biomass conversion into bioethanol. Thus, the aim of the current study is to produce a recombinant β-glycosidase from <i>Moniliophtora perniciosa</i> expressed in <i>Escherichia coli</i> cells. Enzyme coding sequence expression was confirmed through Sanger sequencing after using wheat bran (WB) and carboxymethylcellulose (CMC) as fungal growth media. Synthetic gene betaglyc-GH1 with optimized codons for <i>E. coli</i> expression was cloned in pET-28a. β-glucosidase recombinant (GH1chimera) was purified using a nickel column and its identity was confirmed through mass spectrometry. The recombinant enzyme presented an apparent molecular mass of 53.23 kDa on SDS-PAGE. Recombinant β-glucosidase has shown hydrolytic activity using p-nitrophenyl-β-D-glycopyranoside (pNPG) as substrate and maximum activity at pH 4.6 and 65 °C. Thus, the results indicate that the application of the GH1chimera in the hydrolysis of lignocellulosic materials to obtain glucose monomers can be efficient.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s13205-024-04128-x.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"14 11","pages":"287"},"PeriodicalIF":2.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11530418/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142567187","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":"Novel genetic variants of banana streak MY virus and banana streak IM virus naturally infecting banana in Northeast India.","authors":"Richa Rai, Yumlembam Rupert Anand, Sapam Monteshori, Damini Diksha, Saurabh Kumar Dubey, Virendra Kumar Baranwal, Susheel Kumar Sharma","doi":"10.1007/s13205-024-04113-4","DOIUrl":"10.1007/s13205-024-04113-4","url":null,"abstract":"<p><p>Divergent banana streak viruses (BSV) were characterized from banana plants exhibiting diverse symptoms in the Northeast region (NER) of India. Using rolling circle amplification (RCA), the complete genome sequences of seven episomal banana streak MY virus (BSMYV) isolates, including two novel variants, and two new banana streak IM virus (BSIMV) isolates were characterized. The novel BSMYV genetic variants were associated with conspicuous necrosis on newly emerged leaves, peduncle distortion, pseudostem internal necrosis, in addition to common streak symptoms. For complete genome nucleotide sequences, BSMYV-IN4 and IN5 shared 77-79% identity with other BSMYVs, while BSMYV-IN7 and IN8 exhibited identities of 77-97%. This study reports for the first time, the complete genomes of two banana streak IM virus (BSIMV-IN1 and -IN2) infecting triploid banana hybrids exhibiting leaf distortion, stunted rosette-like growth, and necrosis, sharing 87% sequence identity with reference BSIMV genome (GenBank accession no. HQ593112). Phylogenetic inference based on complete genomes revealed the distinct and congruent placement of BSMYV-IN4 and IN5 within the BSMYV cluster. Pairwise sequence comparisons of the conserved RT/RNase H nucleotide (nt) sequences revealed that the BSMYV-IN7 and IN4 isolates showed 85% and 97% identity to BSMYV (AY805074), respectively, which shared highest nt identity with BSMYV-IN6, IN9, and IN10, at 100%. The RT/RNase H nt sequences of BSIMV-IN1 and IN2 had 98% identity with the BSIMV (HQ593112), but were characterized as novel variants of BSIMV based on complete genomes. An analysis of relative synonymous codon usage (RSCU) pattern in the ORFIII polyprotein of BSMYV and BSIMV isolates revealed AGA and AGG (arginine) as the most frequently overrepresented codons (>1.5), evolutionary conserved in the genome of both species. A total of 14 recombination events were detected among the 36 BSV genomes, with recombination breakpoints mainly located in the ORFI, III, and IGR genomic regions. A novel phylogenetic cluster, comprised of BSMYV-IN4 and IN5 within the clade I was probably derived from heterologous recombination between parents resembling banana streak VN virus (BSVNV; AY750155) and banana streak GF virus (BSGFV; KJ013507) isolates. The present study conclusively reports the infection of genetically and symptomatically distinct variants of BSMYV and BSIMV infecting banana hybrids in NER India.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"14 11","pages":"277"},"PeriodicalIF":2.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11499479/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142492697","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":"Exploring the green synthesis of silver nanoparticles using natural extracts and their potential for cancer treatment.","authors":"Ahmed A H Abdellatif, Mahmoud A H Mostafa, Hiroyuki Konno, Mahmoud A Younis","doi":"10.1007/s13205-024-04118-z","DOIUrl":"10.1007/s13205-024-04118-z","url":null,"abstract":"<p><p>Silver nanoparticles (AgNPs) have attracted increasing attention in nanomedicine, with versatile applications in drug delivery, antimicrobial treatments, and cancer therapies. While chemical synthesis remains a common approach for AgNP production, ensuring environmental sustainability requires a shift toward eco-friendly, \"green\" synthesis techniques. This article underscores the promising role of plant extracts in the green synthesis of AgNPs, highlighting the importance of their natural sources and diverse bioactive compounds. Various characterization methods for these nanomaterials are also reviewed. Furthermore, the anticancer potential of green AgNPs (Gr-AgNPs) is examined, focusing on their mechanisms of action and the challenges to their clinical implementation. Finally, future directions in the field are discussed.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"14 11","pages":"274"},"PeriodicalIF":2.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11496425/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142492766","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":"Phytoplasma etiology and epidemiology of wheat streak and stunting disease in Central India.","authors":"Manish Kumar, T L Prakasha, A N Mishra, M S Saharan, N Meshram, Govind P Rao","doi":"10.1007/s13205-024-04114-3","DOIUrl":"10.1007/s13205-024-04114-3","url":null,"abstract":"<p><p>A total of 151 genotypes of durum and bread wheat exhibiting symptoms of stunting and bushy growth, leaf yellowing, and drying of clumps were recorded at ICAR-IARI Regional Station, Indore, Madhya Pradesh, India from 2016 to 2018. The disease incidence was recorded more in durum wheat genotypes as compared to bread wheat genotypes. The presence of any virus, bacterial, and fungal pathogens was ruled out by applying cultural growth and electron microscopy. However, association of phytoplasmas presence was confirmed in 142 (out of 151) durum and bread wheat genotypes by employing PCR primer pairs of 16S rRNA, <i>leu</i>S and <i>sec</i>A genes. The sequence analysis of all the genes and in silico RFLP analysis of 16S rDNA sequences of wheat phytoplasma strains identified them as rice yellow dwarf group (16SrXI-B) and Bermuda grass white leaf group (16SrXIV-A). Two symptomatic weed species (<i>Parthenium hysterophorus</i> and <i>Cleome gynandra</i>) tested positive for 16SrXI-B phytoplasma subgroup and four weed species (<i>Cynodon dactylon</i>, <i>Digitaria sanguinalis</i>, <i>Euphorbia hirta</i> and <i>Rhynchosia minima</i>) for 16SrXIV-A phytoplasma subgroup growing in and around wheat fields. Six hopper species identified from symptomatic wheat fields were also analyzed for phytoplasma presence. Three hopper species viz., <i>Sogatella furcifera</i>, <i>Balclutha rubrostriata</i>, and <i>Exitianus indicus</i> were tested positive to phytoplasmas in 16SrXIV group, while <i>Sogatella kolophon</i>, <i>Cofana unimaculata</i>, and <i>Maiestas sp.</i> tested positive to 16SrXI group of phytoplasmas in nested PCR assays. Transmission assays revealed that <i>S. furcifera</i> and <i>B. rubrostriata</i> successfully transmitted the 16SrXIV-A strain from infected wheat to healthy wheat plants; however, <i>C. unimaculata</i> was able to transmit 16SrXI-B subgroup from infected wheat to healthy wheat plants under glasshouse conditions. A variation in phytoplasma associated disease incidence was recorded on wheat genotypes in different years and was also found positively correlated with temperature, humidity, and hopper population. The identification of similar phytoplasma strains (16SrXI and 16SrXIV group) from wheat, weeds, and hoppers indicated potential risk of transmission of these strains to wheat genotypes and other agricultural crops, which needs further investigations on epidemiological aspects.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s13205-024-04114-3.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"14 11","pages":"268"},"PeriodicalIF":2.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11473762/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142455473","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":"Comparative genomics of zoonotic pathogen <i>Clostridioides difficile</i> of animal origin to understand its diversity.","authors":"Kumaragurubaran Karthik, Subbaiyan Anbazhagan, Murugaiyan Latha Mala Priyadharshini, Rajeev Kumar Sharma, Seeralan Manoharan","doi":"10.1007/s13205-024-04102-7","DOIUrl":"10.1007/s13205-024-04102-7","url":null,"abstract":"<p><p><i>Clostridioides difficile</i>, a zoonotic pathogen causing enteric diseases in different animals and humans. A comprehensive study on the presence of toxin genes and antimicrobial resistance genes based on genome data of <i>C. difficile</i> in animals is scanty. In the present study, a total of 15 <i>C. difficile</i> isolates were recovered from dogs and isolates with toxin genes (D1, CD15 and CD26) along with two other non-toxigenic strains (CD28, CD32) were used for whole genome sequencing and comparative genomics. Sequence type-based clustering was noted in the whole genome phylogeny with 4 known multi-locus sequence typing (MLST) clades namely I, II, IV, and V and a cryptic clade. ST11 and ST54 were reported for the 2^nd time worldwide in dogs. Out of 109 genomes used in the study, 29 genomes were predicted with all four toxin genes (<i>toxA</i>, <i>toxB</i>, <i>cdtA</i>, <i>cdtB</i>) while 22 did not have any of the toxin genes. ST11 of MLST clade V had the maximum number of 46 genomes predicted with at least one toxin gene. Among the genomes sequenced in this study, CD26 had a maximum of 5 AMR genes (<i>aac(6')-aph(2″)</i>, <i>ant(6)-Ia</i>, <i>catP</i>, <i>erm(B)_18</i>, and <i>tet(M)_11</i>) and CD15 was predicted with 2 AMR genes (<i>aac(6')-aph(2″)</i>, <i>erm(B)_18</i>). Tetracycline resistance genes were predicted most in the ST11 genome. Of the 22 non-toxigenic strains, 9 genomes (ST48 = 5, ST3 = 2, ST109 = 1, ST15 = 1) were predicted with a minimum of one AMR gene. Pangenome analysis indicated that the <i>Bpan</i> value is 0.12 showing that <i>C. difficile</i> has an open pangenome structure. This indicates that the organism can evolve by the addition of new genes. This study reports the circulation of clinically important ST11 and multidrug-resistant non-toxigenic strains among animals.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s13205-024-04102-7.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"14 11","pages":"257"},"PeriodicalIF":2.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11452369/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142379857","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":"In vitro and in vivo study of the antagonistic effects of a Trichoderma strain against four isolates of Fusarium that are pathogenic to chickpea.","authors":"Manal Adnani, Naila El Hazzat, Moulay Abdelaziz El Alaoui, Karima Selmaoui, Rachid Benkirane, Amina Ouazzani Touhami, Allal Douira","doi":"10.1007/s13205-024-04112-5","DOIUrl":"10.1007/s13205-024-04112-5","url":null,"abstract":"<p><p>This study investigated the antagonistic activity of <i>Trichoderma asperellum</i> against chickpea <i>Fusarium</i> wilt through in vitro and in vivo experiments. The dual culture test showed that <i>Trichoderma</i> had a significant inhibitory effect on the growth of the tested <i>Fusarium</i> isolates, with an inhibition rate ranging from 71.33% to 80.66%. The volatile and non-volatile metabolites produced by <i>Trichoderma</i> also showed antagonistic effects, with a growth inhibition rate ranging from 47.33% to 51.33% and a colonization rate ranging from 60% to 67%. In vivo experiments demonstrated that treating chickpea seeds with <i>Trichoderma asperellum</i> 48 h after inoculation with Fusarium significantly enhanced chickpea growth compared to seeds inoculated with <i>Fusarium</i> alone. Arial part length enhancement ranged between 69.3% and 92,19% while root length increased by 61,9% and 127%, this implied a significant improvement in biomass. These findings highlight <i>Trichoderma</i>'s potential in controlling chickpea <i>Fusarium</i> wilt and enhancing plant growth, making it an environmentally friendly method in sustainable agriculture and crop protection.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"14 11","pages":"271"},"PeriodicalIF":2.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11489381/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142455455","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":"The effects of irrigation on the survival of <i>Clostridium sporogenes</i> in the phyllosphere and soil environments of lettuce.","authors":"Johannes Cornelius Jacobus Fourie, Deidre Van Wyk, Cornelius Carlos Bezuidenhout, Charlotte Mienie, Rasheed Adeleke","doi":"10.1007/s13205-024-04069-5","DOIUrl":"10.1007/s13205-024-04069-5","url":null,"abstract":"<p><p>This study aimed to address the gap in knowledge regarding the fate of foodborne pathogens within agro-ecosystems. It specifically focused on the surrogate microorganism <i>Clostridium sporogenes</i>, which was introduced into lettuce-producing environments via surface and spray irrigation methods, respectively. The concentration of <i>C. sporogenes</i> in the rhizosphere, phyllosphere, and non-rhizosphere soil was quantified by quantitative polymerase chain reaction (qPCR) over a 42-day trial. The surface irrigation method exhibited a more noticeable contamination effect on the soil environments, compared to the phyllosphere. The results indicated a noticeable increase in <i>C. sporogenes</i> concentrations during the initial 22 days, with a 10.4-fold rise (0.39-4.05 log copy numbers/g soil) in the rhizosphere and 1.9-fold increase (2.97-5.59 log copy numbers/g soil) in the non-rhizosphere. However, concentrations in both soil environments subsequently decreased, falling below the initial inoculum concentration by the end of the trial. In contrast, the spray irrigation method resulted in most of the contamination being localised on the lettuce phyllosphere, with a high <i>C. sporogenes</i> concentration of 9.09 log copy numbers/g leaves on day 0. This concentration exponentially decreased to a minimal 0.019 log copy numbers/g leaves by day 32. Although concentrations in both soil environments decreased over time, trace concentrations of <i>C. sporogenes</i> were detectable at the end of the trial, posing a potential hazard to the microbiological safety of postharvest produce. These findings shed light on the dynamics of <i>C. sporogenes</i> in agro-ecosystems and underscore the importance of irrigation practices that ensure the safety of those who consume fresh produce.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s13205-024-04069-5.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"14 10","pages":"239"},"PeriodicalIF":2.6,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11415320/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142278671","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}