Microbiological research最新文献

{"title":"Adaptability of the gut microbiota of the German cockroach Blattella germanica to a periodic antibiotic treatment","authors":"Jesús Marín-Miret ,&nbsp;Ana Elena Pérez-Cobas ,&nbsp;Rebeca Domínguez-Santos ,&nbsp;Benjamí Pérez-Rocher ,&nbsp;Amparo Latorre ,&nbsp;Andrés Moya","doi":"10.1016/j.micres.2024.127863","DOIUrl":"10.1016/j.micres.2024.127863","url":null,"abstract":"<div><p>High-throughput sequencing studies have shown that diet or antimicrobial treatments impact animal gut microbiota equilibrium. However, properties related to the gut microbial ecosystem stability, such as resilience, resistance, or functional redundancy, must be better understood. To shed light on these ecological processes, we combined advanced statistical methods with 16 S rRNA gene sequencing, functional prediction, and fitness analyses in the gut microbiota of the cockroach <em>Blattella germanica</em> subject to three periodic pulses of the antibiotic (AB) kanamycin (n=512). We first confirmed that AB did not significantly affect cockroaches' biological fitness, and gut microbiota changes were not caused by insect physiology alterations. The sex variable was examined for the first time in this species, and no statistical differences in the gut microbiota diversity or composition were found. The comparison of the gut microbiota dynamics in control and treated populations revealed that (1) AB treatment decreases diversity and completely disrupts the co-occurrence networks between bacteria, significantly altering the gut community structure. (2) Although AB also affected the genetic composition, functional redundancy would explain a smaller effect on the functional potential than on the taxonomic composition. (3) As predicted by Taylor's law, AB generally affected the most abundant taxa to a lesser extent than the less abundant taxa. (4) Taxa follow different trends in response to ABs, highlighting \"resistant taxa,\" which could be critical for community restoration. (5) The gut microbiota recovered faster after the three AB pulses, suggesting that gut microbiota adapts to repeated treatments.</p></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0944501324002647/pdfft?md5=52a39a5bc48555f022c32d60933a4cf0&pid=1-s2.0-S0944501324002647-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141897757","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unravelling the secondary metabolome and biocontrol potential of the recently described species Bacillus nakamurai","authors":"François Nimbeshaho ,&nbsp;Gaspard Nihorimbere ,&nbsp;Anthony Argüelles Arias ,&nbsp;Charlotte Liénard ,&nbsp;Sébastien Steels ,&nbsp;Anaclet Nibasumba ,&nbsp;Venant Nihorimbere ,&nbsp;Anne Legrève ,&nbsp;Marc Ongena","doi":"10.1016/j.micres.2024.127841","DOIUrl":"10.1016/j.micres.2024.127841","url":null,"abstract":"<div><p>In the prospect of novel potential biocontrol agents, a new strain BDI-IS1 belonging to the recently described <em>Bacillus nakamurai</em> was selected for its strong <em>in vitro</em> antimicrobial activities against a range of bacterial and fungal phytopathogens. Genome mining coupled with metabolomics revealed that BDI-IS1 produces multiple non-ribosomal secondary metabolites including surfactin, iturin A, bacillaene, bacillibactin and bacilysin, together with some some ribosomally-synthesized and post-translationally modified peptides (RiPPs) such as plantazolicin, and potentially amylocyclicin, bacinapeptin and LCI. Reverse genetics further showed the specific involvement of some of these compounds in the antagonistic activity of the strain. Comparative genomics between the five already sequenced <em>B. nakamurai</em> strains showed that non-ribosomal products constitute the core metabolome of the species while RiPPs are more strain-specific. Although the secondary metabolome lacks some key bioactive metabolites found in <em>B. velezensis</em>, greenhouse experiments show that <em>B. nakamurai</em> BDI-IS1 is able to protect tomato and maize plants against early blight and northern leaf blight caused by <em>Alternaria solani</em> and <em>Exserohilum turcicum</em>, respectively, at levels similar to or better than <em>B. velezensis</em> QST713. The reduction of these foliar diseases, following root or leaf application of the bacterial suspension demonstrates that BDI-IS1 can act by direct antibiosis and by inducing plant defence mechanisms. These findings indicate that <em>B. nakamurai</em> BDI-IS1 can be considered as a good candidate for biocontrol of plant diseases prevailing in tropical regions, and encourage further research into its spectrum of activity, its requirements and the conditions needed to ensure its efficacy.</p></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0944501324002428/pdfft?md5=fffc26b9c220475bd011d61204b1e754&pid=1-s2.0-S0944501324002428-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141993244","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Endophytic microbial diversity associated with commercial cultivar and crop wild relative banana variety could provide clues for microbial community management","authors":"Luisa F. Posada ,&nbsp;Luis A. Arteaga-Figueroa ,&nbsp;Isabel Adarve-Rengifo ,&nbsp;Maria Cadavid ,&nbsp;Sebastián Zapata ,&nbsp;Javier C. Álvarez","doi":"10.1016/j.micres.2024.127862","DOIUrl":"10.1016/j.micres.2024.127862","url":null,"abstract":"<div><p>Endophytes, microorganisms inhabiting internal plant tissues, play a pivotal role in plant growth and disease resistance. Moreover, previous studies have established that <em>Musa</em> plants derive disease protective functions from their microbiome. Notably, one of the crop wild relatives of banana, the Calcutta 4 variety, exhibits resistance to various phytopathogens such as <em>Pseudocercospora fijiensis</em> (<em>P. fijiensis</em>), while the Williams commercial cultivar (cv.) is highly susceptible. Therefore, this study aims primarily to characterize and compare the endophytic microbiota composition of Calcutta 4 and Williams banana plants when grown sympatrically. Alongside, differences in endophytic microbiome between plant sections (shoot or roots), growth phases (<em>in vitro</em> or greenhouse) and fitness factors such as the addition of plant growth-promoting bacteria <em>Bacillus subtilis</em> EA-CB0575 (T2 treatment) or infection by <em>P. fijiensis</em> (T3 treatment) were examined. Both culture-dependent and -independent techniques were used to evaluate these differences and assess the culturability of banana endophytes under varying conditions. Microbial cultures resulted in 331 isolates distributed across 54 genera when all treatments were evaluated, whereas <em>16 S</em> sequencing produced 9510 ASVs assigned in 1456 genera. Alpha and beta diversity exhibited significant differences based on plant section, with an increase in phylogenetic diversity observed in plants with pathogen infection (T3) compared to control plants (T1). Additionally, four differentially abundant genera associated with nitrogen metabolism were identified in T3 plants and seven genera showed differential abundance when comparing varieties. When culture-dependent and -independent methods were compared, it was found that isolates represented 3.7 % of the genera detected by culture-independent methods, accounting for 12–41 % of the total data depending on the treatment. These results are crucial for proposing management strategies derived from crop wild relatives to enhance the resilience of susceptible commercial varieties against fitness factors affecting crop development. Additionally, they help to decipher the pathogenic effects of <em>P. fijiensis</em> in banana plants and advance the understanding of how plant domestication influences the endosphere.</p></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0944501324002635/pdfft?md5=eb55da9021cbfb39c09200c035c60b1e&pid=1-s2.0-S0944501324002635-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141913289","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A combination of physiology, metabolomics, and genetics reveals the two-component system ResS/ResR-mediated Fe and Al release from biotite by Pseudomonas pergaminensis F77","authors":"Wen Dong ,&nbsp;Qiyu Xiang ,&nbsp;Hui Zhao ,&nbsp;Qi Sheng ,&nbsp;Linyan He ,&nbsp;Xiafang Sheng","doi":"10.1016/j.micres.2024.127861","DOIUrl":"10.1016/j.micres.2024.127861","url":null,"abstract":"<div><p>Understanding of the mechanisms on bacteria-regulated mineral dissolution functions is important for further insight into mineral-microbe interactions. The functions of the two-component system have been studied. However, the molecular mechanisms involved in bacterial two-component system-mediated mineral dissolution are poorly understood. Here, the two-component regulatory system ResS/ResR in the mineral-solubilizing bacterium <em>Pseudomonas pergaminensis</em> F77 was characterized for its involvement in biotite dissolution. Strain F77 and the F77Δ<em>resS</em>, F77Δ<em>resR</em>, and F77Δ<em>resS/R</em> mutants were constructed and compared for the ResS/ResR system-mediated Fe and Al release from biotite in the medium and the mechanisms involved. After 3 days of incubation, the F77Δ<em>resS</em>, F77Δ<em>resR</em>, and F77Δ<em>resS/R</em> mutants significantly decreased the Fe and Al concentrations in the medium compared with F77. The F77Δ<em>resS/R</em> mutant had a greater impact on Fe and Al release from biotite than did the F77Δ<em>resS</em> or F77Δ<em>resR</em> mutant. The F77∆<em>resS/R</em> mutant exhibited significantly reduced Fe and Al concentrations by 21–61 % between 12 h and 48 h of incubation compared with F77. Significantly increased pH values and decreased cell counts on the mineral surfaces were found in the presence of the F77∆<em>resS/R</em> mutant compared with those in the presence of F77 between 12 h and 48 h of incubation. Metabolomic analysis revealed that the extracellular metabolites associated with biotite dissolution were downregulated in the F77Δ<em>resS/R</em> mutant. These downregulated metabolites included GDP-fucose, 20-carboxyleukotriene B4, PGP (16:1(9Z)/16:0), 3′,5′-cyclic AMP, and a variety of acidic metabolites involved in carbohydrate, amino acid, and lipid metabolisms, glycan biosynthesis, and cellular community function. Furthermore, the expression levels of the genes involved in the production of these metabolites were downregulated in the F77Δ<em>resS/R</em> mutant compared with those in F77. Our findings suggested that the ResS/ResR system in F77 contributed to mineral dissolution by mediating the production of mineral-solubilizing related extracellular metabolites and bacterial adsorption on mineral surface.</p></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141879102","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"BrfA functions as a bacterial enhancer-binding protein to regulate functional amyloid Fap-dependent biofilm formation in Pseudomonas fluorescens by sensing cyclic diguanosine monophosphate","authors":"Miao Guo ,&nbsp;Siqi Tan ,&nbsp;Yinying Wu ,&nbsp;Chongni Zheng ,&nbsp;Peng Du ,&nbsp;Junli Zhu ,&nbsp;Aihua Sun ,&nbsp;Xiaoxiang Liu","doi":"10.1016/j.micres.2024.127864","DOIUrl":"10.1016/j.micres.2024.127864","url":null,"abstract":"<div><p>The functional amyloid of <em>Pseudomonas</em> (Fap) is essential for the formation of macrocolony biofilms, pellicles, and solid surface-associated (SSA) biofilms of <em>Pseudomonas fluorescens</em> PF07, an isolate from refrigerated marine fish. However, limited information on the expression regulation of <em>fap</em> genes is available. Herein, we found that a novel bacterial enhancer-binding protein (bEBP), BrfA, regulated Fap-dependent biofilm formation by directly sensing cyclic diguanosine monophosphate (c-di-GMP). Our <em>in vivo</em> data showed that the REC domain deletion of BrfA promoted <em>fap</em> gene expression and biofilm formation, and c-di-GMP positively regulated the transcription of <em>fapA</em> in a BrfA-dependent manner. In <em>in vitro</em> experiments, we found that the ATPase activity of BrfA was inhibited by the REC domain and was activated by c-di-GMP. BrfA and the sigma factor RpoN bound to the upstream region of <em>fapA</em>, and the binding ability of BrfA was not affected by either deletion of the REC domain or c-di-GMP. BrfA specifically bound to the three enhancer sites upstream of the <em>fapA</em> promoter, which contain the consensus sequence CA-(N4)-TGA(A/T)ACACC. <em>In vivo</em> experiments using a <em>lacZ</em> fusion reporter indicated that all three BrfA enhancer sites were essential for the activation of <em>fapA</em> transcription. Overall, these findings reveal that BrfA is a new type of c-di-GMP-responsive transcription factor that directly controls the transcription of Fap biosynthesis genes in <em>P</em>. <em>fluorescens</em>. Fap functional amyloids and BrfA-type transcription factors are widespread in <em>Pseudomonas</em> species. The novel insights into the c-di-GMP- and BrfA-dependent expression regulation of <em>fap</em> provided by this work will contribute to the development of antibiofilm strategies.</p></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141907050","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rhizosphere microbiome assembly, drivers and functions in perennial ligneous plant health","authors":"Morgane Duret ,&nbsp;Adrian Wallner ,&nbsp;Marc Buée ,&nbsp;Aziz Aziz","doi":"10.1016/j.micres.2024.127860","DOIUrl":"10.1016/j.micres.2024.127860","url":null,"abstract":"<div><p>Plants shape and interact continuously with their rhizospheric microbiota, which play a key role in plant health and resilience. However, plant-associated microbial community can be shaped by several factors including plant phenotype and cropping system. Thus, understanding the interplay between microbiome assembly during the onset of plant-pathogen interactions and long-lasting resistance traits in ligneous plants remains a major challenge. To date, such attempts were mainly investigated in herbaceous plants, due to their phenotypic characteristics and their short life cycle. However, only few studies have focused on the microbial structure, dynamic and their drivers in perennial ligneous plants. Ligneous plants coevolved in interaction with specific fungal and bacterial communities that differ from those of annual plants. The specificities of such ligneous plants in shaping their own functional microbial communities could be dependent on their high heterozygosis, physiological and molecular status associated to seasonality and their aging processes, root system and above-ground architectures, long-lasting climatic variations, and specific cultural practices. This article provides an overview of the specific characteristics of perennial ligneous plants that are likely to modulate symbiotic interactions in the rhizosphere, thus affecting the plant’s fitness and systemic immunity. Plant and microbial traits contributing to the establishment of plant-microbiome interactions and the adaptation of this holobiont are also discussed.</p></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0944501324002611/pdfft?md5=3f7334e0062208b074bbc822eca1bfa4&pid=1-s2.0-S0944501324002611-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141868990","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"BmfR, a novel GntR family regulator, regulates biofilm formation in marine-derived, Bacillus methylotrophicus B-9987","authors":"Shanshan Xu ,&nbsp;Zengzhi Liu ,&nbsp;Pengfei Ren ,&nbsp;Yang Liu ,&nbsp;Fei Xiao ,&nbsp;Wenli Li","doi":"10.1016/j.micres.2024.127859","DOIUrl":"10.1016/j.micres.2024.127859","url":null,"abstract":"<div><p>Biofilms are common living states for microorganisms, allowing them to adapt to environmental changes. Numerous <em>Bacillus</em> strains can form complex biofilms that play crucial roles in biocontrol processes. However, our current understanding of the molecular mechanisms of biofilm formation in <em>Bacillus</em> is mainly based on studies of <em>Bacillus subtilis.</em> Knowledge regarding the biofilm formation of other <em>Bacillus</em> species remains limited. In this study, we identified a novel transcriptional regulator, BmfR, belonging to the GntR family, that regulates biofilm formation in marine-derived <em>Bacillus methylotrophicus</em> B-9987. We demonstrated that BmfR induces biofilm formation by activating the extracellular polysaccharide structural genes <em>epsA-O</em> and negatively regulating the matrix gene repressor, SinR; of note it positively affects the expression of the master regulator of sporulation, Spo0A. Furthermore, database mining for BmfR homologs has revealed their widespread distribution among many bacterial species, mainly Firmicutes and Proteobacteria. This study advances our understanding of the biofilm regulatory network of <em>Bacillus</em> strains, and provides a new target for exploiting and manipulating biofilm formation.</p></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141841496","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gut microbiota modulates neurotransmitter and gut-brain signaling","authors":"Shiyan Qu ,&nbsp;Zijin Yu ,&nbsp;Yaxuan Zhou ,&nbsp;Shiyi Wang ,&nbsp;Minqi Jia ,&nbsp;Ti Chen ,&nbsp;Xiaojie Zhang","doi":"10.1016/j.micres.2024.127858","DOIUrl":"10.1016/j.micres.2024.127858","url":null,"abstract":"<div><p>Neurotransmitters, including 5-hydroxytryptamine (5-HT), dopamine (DA), gamma-aminobutyric acid (GABA), and glutamate, are essential transductors in the Gut-Brain Axis (GBA), playing critical roles both peripherally and centrally. Accumulating evidence suggests that the gut microbiota modulates intestinal neurotransmitter metabolism and gut-to-brain signaling, shedding light on the crucial role of the gut microbiota in brain function and the pathogenesis of various neuropsychiatric diseases, such as major depression disorder (MDD), anxiety, addiction and Parkinson's disease (PD). Despite the exciting findings, the mechanisms underlying the modulation of neurotransmitter metabolism and function by the gut microbiota are still being elucidated. In this review, we aim to provide a comprehensive overview of the existing knowledge about the role of the gut microbiota in neurotransmitter metabolism and function in animal and clinical experiments. Moreover, we will discuss the potential mechanisms through which gut microbiota-derived neurotransmitters contribute to the pathogenesis of neuropsychiatric diseases, thus highlighting a novel therapeutic target for these conditions.</p></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141850631","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cervicovaginal microbiome, high-risk HPV infection and cervical cancer: Mechanisms and therapeutic potential","authors":"Roujie Huang ,&nbsp;Zimo Liu ,&nbsp;Tianshu Sun ,&nbsp;Lan Zhu","doi":"10.1016/j.micres.2024.127857","DOIUrl":"10.1016/j.micres.2024.127857","url":null,"abstract":"<div><p>The microbiota in the female genital tract is an intricate assembly of diverse aerobic, anaerobic, and microaerophilic microorganisms, which share the space within the reproductive tract and engage in complex interactions. Microbiome dysbiosis may disrupt the symbiotic relationship between the host and microorganisms and play a pivotal role in the pathogenesis of various diseases, including its involvement in the establishment of human papillomavirus (HPV)-associated cervical cancer (CC). Interventions to restore microbiota homeostasis (e.g., probiotics) and bacterial-vector HPV therapeutic vaccines have been reported to be potentially effective in clearing HPV infection and ameliorating cytological abnormalities. In this review, we place emphasis on elucidating the alterations within the cervical–vaginal microbiota as well as the intratumoral microbiota in the context of high-risk HPV (HR-HPV) infection and its subsequent progression to cervical intraepithelial neoplasia/CC. Furthermore, we explore the mechanisms by which these microbial communities exert potential pathogenic or protective effects, including modulating genital inflammation and immune responses, affecting HR-HPV oncogene expression and oncoprotein production, regulating oxidative stress and deoxyribonucleic acid (DNA) damage, and inducing metabolic rewiring. Lastly, we summarize the latest evidence in human trials regarding the efficacy of probiotics, prebiotics and probiotic-vector HPV therapeutic vaccines. This review aims to foster a deeper understanding of the role of the microbiota in HR-HPV infection-related cervix cancer development, and further provide a theoretical basis for the development of preventive and therapeutic strategies based on microbial modulation.</p></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0944501324002581/pdfft?md5=512d9986f5f6bdf21960bfbef1a95b3c&pid=1-s2.0-S0944501324002581-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141840974","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multi-omics analysis reveals the effects of three application modes of plant growth promoting microbes biofertilizer on potato (Solanum tuberosum L.) growth under alkaline loess conditions","authors":"Yuan Tian ,&nbsp;Yang Liu ,&nbsp;Liang Yue ,&nbsp;Xia Zhao ,&nbsp;Qin Zhou ,&nbsp;Constantine Uwaremwe ,&nbsp;Yun Wang ,&nbsp;Gaofeng Chen ,&nbsp;Yuexia Sha ,&nbsp;Yubao Zhang ,&nbsp;Ruoyu Wang","doi":"10.1016/j.micres.2024.127855","DOIUrl":"10.1016/j.micres.2024.127855","url":null,"abstract":"<div><p>Potato is an important crop due to its high contents of starch, protein, and various vitamins and minerals. Biofertilizers are composed of plant growth promoting microbes (PGPMs) which are essential for improving the growth and resistance of potato. However, little information has focused on the modes of inoculation of biofertilizers on plant growth and microecology. This study aims to reveal the response mechanism of the potato to three modes of inoculation of biofertilizers all containing PGPM <em>Bacillus amyloliquefaciens</em> EZ99, i.e. scattered mode of 5 kg/ha biofertilizer (M5), soaking seed tubers with dissolved 5 kg/ha biofertilizer (MZG), and scattered mode of 3 kg/ha biofertilizer + 2 kg/ha sucrose (MY34) in alkaline loess field through multi-omics analysis of transcriptome, metabolome and microbiome. The physiological result revealed that two application modes of equal amount of biofertilizer M5 and MZG significantly improved the growth and yield of potatoes. Furthermore, the transcriptome of potato exhibited sets of differentially expressed genes enriched in photosynthesis, sugar metabolism, and phenylpropanoid biosynthesis among the three modes, with the M5 mode exhibiting overall up-regulation of 828 genes. Based on the untargeted metabolomic analysis of potato tuber, M5 mode significantly accumulated sucrose, while MZG and MY34 mode significantly accumulated the stress metabolites euchrenone b6 and mannobiose, respectively. Besides, the microbial structure of potato rhizosphere showed that the diversity of bacteria and fungi was similar in all soils, but their abundances varied significantly. Specifically, beneficial <em>Penicillium</em> was enriched in M5 and MZG soils<em>,</em> whereas MY34 soil accumulated potential pathogens <em>Plectosphaerella</em> and saccharophilic <em>Mortierella</em>. Collectively, these e findings highlight that MZG is the most effective mode to promote potato growth and stimulate rhizosphere effect. The present study not only encourages sustainable agriculture through agroecological practices, but also provides broad prospects for the application of PGPM biofertilizer in staple foods.</p></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141840134","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}