Pub Date : 2024-11-02DOI: 10.1016/j.micres.2024.127956
Linlin Yao , Junwei Zheng , Bin Wang , Li Pan
Aspergillus niger is a powerful and efficient cell factory, with the potential to synthesize valuable products as chassis cells. The use of microbial cell factories to produce monacolin J, a precursor for statin synthesis, as an alternative to chemical synthesis could meet increasing market demand. However, the need for precise large fragment gene editing and the availability of suitable integration loci hinders the application of this strain. Herein, we identified neutral integration sites of A. niger based on the combination of ATAC-seq, H3K4me3 epigenetic datasets. Next, a landing pad system was developed for the one-step integration of the MJ biosynthesis gene cluster (BGC) in A. niger. Furthermore, we optimized the precursor module supply, the auxiliary factor supply module of NADPH, the module for eliminating oxidative stress pressure, and the transporter module to improve the production of MJ. Finally, a multi-copy integration strategy was applied to the rapid integration of MJ BGC, achieving MJ titer up to 1851.52 mg/L at the 500 mL shaker level.
{"title":"Development of a landing pad system for Aspergillus niger and its application in the overproduction of monacolin J","authors":"Linlin Yao , Junwei Zheng , Bin Wang , Li Pan","doi":"10.1016/j.micres.2024.127956","DOIUrl":"10.1016/j.micres.2024.127956","url":null,"abstract":"<div><div><em>Aspergillus niger</em> is a powerful and efficient cell factory, with the potential to synthesize valuable products as chassis cells. The use of microbial cell factories to produce monacolin J, a precursor for statin synthesis, as an alternative to chemical synthesis could meet increasing market demand. However, the need for precise large fragment gene editing and the availability of suitable integration loci hinders the application of this strain. Herein, we identified neutral integration sites of <em>A. niger</em> based on the combination of ATAC-seq, H3K4me3 epigenetic datasets. Next, a landing pad system was developed for the one-step integration of the MJ biosynthesis gene cluster (BGC) in <em>A. niger</em>. Furthermore, we optimized the precursor module supply, the auxiliary factor supply module of NADPH, the module for eliminating oxidative stress pressure, and the transporter module to improve the production of MJ. Finally, a multi-copy integration strategy was applied to the rapid integration of MJ BGC, achieving MJ titer up to 1851.52 mg/L at the 500 mL shaker level.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"290 ","pages":"Article 127956"},"PeriodicalIF":6.1,"publicationDate":"2024-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142604110","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}
Pub Date : 2024-10-31DOI: 10.1016/j.micres.2024.127961
Guoxu Ao , Changli Wang , Liguo Yang , Yue Ma , Zhaoxuan Wang , Yueqi Shi , Shanshan Sun , Wenxiang Ping
Competition phenomenon is widely presented in nature, however, few reports on the competition phenomenon between bacteria based on the perspective of quorum sensing (QS), especially between Gram-positive bacteria. Here, the Gram-positive bacteria Rhodococcus sp. HD1 and Microbacterium sp. HM-2 were co-cultured, and the epiphysiological indicators, transcriptomics combined with gene engineering technique were applied to clarify the role of QS in the competition between Gram-positive bacteria. The results showed that the morphology of strain HD1 was changed into ellipsoids from long rods, the surface-to-volume ratio increased, and the competition index increased within strains HM-2 and HD1. The biomass of strain HD1(8.06×107 CFU/mL) was decreased significantly (p＜0.05) under co-culture system, compared with mono-culture (5.75×108 CFU/mL), indicating that strain HM-2 had an inhibitory effect on HD1 at 12 h. Transcriptomic analysis revealed that QS-related genes were highly expressed in strain HM-2, and the expression level of the virulence gene TM_0352 was the highest (FPKM: 1774.19). Meanwhile, the ABC transporters-related genes in strain HD1 were significantly increased. Furthermore, QS pathway-related genes in strain HM-2 and ABC transporters-related genes in strain HD1 showed a significant correlation with the gene TM_0352 expression by the Mantel test analysis (p<0.05), surmising that the TM_0352 gene played a dominant role in the co-culture system. Knockout and complementation experiments confirmed that the function of gene TM_0352. The structural equation model showed that the QS up-regulation of strain HM-2 significantly promoted the expression of virulence genes, while strain HD1 promoted ABC transporters to cope with the up-regulation of TM_0352. The up-regulation of TM_0352 promoted the biomass of strain HM-2 and inhibited the biomass of HD1.The above results displayed that the competition phenomenon appeared by QS driving the up-regulation of TM_0352 gene in strain HM-2, which led to the up-regulation of ABC transporters in strain HD1. And these findings provided new insights into the perspective of factors related to competition inhibition between bacteria.
{"title":"Quorum sensing: the “switch” in the competitive relationship between Gram-positive bacteria based on transcriptomic analysis","authors":"Guoxu Ao , Changli Wang , Liguo Yang , Yue Ma , Zhaoxuan Wang , Yueqi Shi , Shanshan Sun , Wenxiang Ping","doi":"10.1016/j.micres.2024.127961","DOIUrl":"10.1016/j.micres.2024.127961","url":null,"abstract":"<div><div>Competition phenomenon is widely presented in nature, however, few reports on the competition phenomenon between bacteria based on the perspective of quorum sensing (QS), especially between Gram-positive bacteria. Here, the Gram-positive bacteria <em>Rhodococcus</em> sp. HD1 and <em>Microbacterium</em> sp<em>.</em> HM-2 were co-cultured, and the epiphysiological indicators, transcriptomics combined with gene engineering technique were applied to clarify the role of QS in the competition between Gram-positive bacteria. The results showed that the morphology of strain HD1 was changed into ellipsoids from long rods, the surface-to-volume ratio increased, and the competition index increased within strains HM-2 and HD1. The biomass of strain HD1(8.06×10<sup>7</sup> CFU/mL) was decreased significantly (<em>p</em>＜0.05) under co-culture system, compared with mono-culture (5.75×10<sup>8</sup> CFU/mL), indicating that strain HM-2 had an inhibitory effect on HD1 at 12 h. Transcriptomic analysis revealed that QS-related genes were highly expressed in strain HM-2, and the expression level of the virulence gene <em>TM_0352</em> was the highest (FPKM: 1774.19). Meanwhile, the ABC transporters-related genes in strain HD1 were significantly increased. Furthermore, QS pathway-related genes in strain HM-2 and ABC transporters-related genes in strain HD1 showed a significant correlation with the gene <em>TM_0352</em> expression by the Mantel test analysis (<em>p</em><0.05), surmising that the <em>TM_0352</em> gene played a dominant role in the co-culture system. Knockout and complementation experiments confirmed that the function of gene <em>TM_0352</em>. The structural equation model showed that the QS up-regulation of strain HM-2 significantly promoted the expression of virulence genes, while strain HD1 promoted ABC transporters to cope with the up-regulation of <em>TM_0352</em>. The up-regulation of <em>TM_0352</em> promoted the biomass of strain HM-2 and inhibited the biomass of HD1.The above results displayed that the competition phenomenon appeared by QS driving the up-regulation of <em>TM_0352</em> gene in strain HM-2, which led to the up-regulation of ABC transporters in strain HD1. And these findings provided new insights into the perspective of factors related to competition inhibition between bacteria.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"290 ","pages":"Article 127961"},"PeriodicalIF":6.1,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142591183","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}
Pub Date : 2024-10-31DOI: 10.1016/j.micres.2024.127962
Yuxuan Liang , Xinyue Liu , Haozhen Chang , Jim Yap , Weining Sun , Haichun Gao
As nitrite, sulfite has been used in food preservation for centuries but how it inhibits bacterial growth remains underexplored. To address this issue, in this study, we set out to test if cytochrome (cyt) c proteins protect bacteria from the damage of certain reactive sulfur species (RSS) because they do so in the case of reactive nitrogen species (RNS). We show that some reactive sulfur species, such as sulfite and peroxymonosulfate (PMS), inhibit growth of bacterial strains devoid of cytochrome (cyt) c proteins. Subsequent investigations link the inhibition of sulfite/PMS to activity of cbb3-type heme-copper oxidase (cbb3-HCO). However, in vitro comparative analysis rules out that either cbb3-HCO or cyt bd oxidase is the primary target of sulfite/PMS. Instead, we found that sulfite/PMS and the cbb3-HCO loss regulate intracellular redox status in a similar manner, by affecting GSH/GSSG homeostasis. The link between the GSH/GSSG homeostasis and sulfite/PMS is further substantiated by using the mutants with enhanced GSSG generation. Furthermore, we present the data to show that inhibitory effects of nitrite and sulfite/PMS are additive although the overall effects may vary depending on species. Our results open an avenue to control bacteria by developing more robust agents that modulating intracellular redox status, which may be used in combination with nitrite as a promising antimicrobial strategy.
{"title":"Inhibitory effects of nitrite and sulfite/peroxymonosulfate on bacteria are mediated respectively through respiration and intracellular GSH homeostasis","authors":"Yuxuan Liang , Xinyue Liu , Haozhen Chang , Jim Yap , Weining Sun , Haichun Gao","doi":"10.1016/j.micres.2024.127962","DOIUrl":"10.1016/j.micres.2024.127962","url":null,"abstract":"<div><div>As nitrite, sulfite has been used in food preservation for centuries but how it inhibits bacterial growth remains underexplored. To address this issue, in this study, we set out to test if cytochrome (cyt) <em>c</em> proteins protect bacteria from the damage of certain reactive sulfur species (RSS) because they do so in the case of reactive nitrogen species (RNS). We show that some reactive sulfur species, such as sulfite and peroxymonosulfate (PMS), inhibit growth of bacterial strains devoid of cytochrome (cyt) <em>c</em> proteins. Subsequent investigations link the inhibition of sulfite/PMS to activity of <em>cbb</em><sub>3</sub>-type heme-copper oxidase (<em>cbb</em><sub>3</sub>-HCO). However, in vitro comparative analysis rules out that either <em>cbb</em><sub>3</sub>-HCO or cyt <em>bd</em> oxidase is the primary target of sulfite/PMS. Instead, we found that sulfite/PMS and the <em>cbb</em><sub>3</sub>-HCO loss regulate intracellular redox status in a similar manner, by affecting GSH/GSSG homeostasis. The link between the GSH/GSSG homeostasis and sulfite/PMS is further substantiated by using the mutants with enhanced GSSG generation. Furthermore, we present the data to show that inhibitory effects of nitrite and sulfite/PMS are additive although the overall effects may vary depending on species. Our results open an avenue to control bacteria by developing more robust agents that modulating intracellular redox status, which may be used in combination with nitrite as a promising antimicrobial strategy.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"290 ","pages":"Article 127962"},"PeriodicalIF":6.1,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142569062","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}
Pub Date : 2024-10-31DOI: 10.1016/j.micres.2024.127960
Xin Shen , Feiyan Zhao , Zhixin Zhao , Jie Yu , Zhihong Sun
Diabetes mellitus (DM) is a common metabolic disease and one of the diseases with the highest number of complications at present. As the disease progresses, patients will gradually develop diabetes-related cognitive decline, mild cognitive impairment (MCI) or even dementia. The occurrence of diabetes-combined cognitive impairment undoubtedly imposes a heavy burden on patients and their families. Current research suggests that risk factors such as blood glucose levels, insulin resistance, oxidative stress and neuroinflammation have an important role in the development of diabetic cognitive impairment (DCI). With the development of technology and in-depth research, the relationship between the two-way communication between the gut and the brain has been gradually revealed, and more studies have found that the gut microbiota plays an important role in the development of DCI. This review explores the feasibility of probiotics as a potential strategy to assist in the improvement of DCI and its potential mechanisms from the perspective of the factors affecting DCI.
{"title":"Probiotics: A potential strategy for improving diabetes mellitus complicated with cognitive impairment","authors":"Xin Shen , Feiyan Zhao , Zhixin Zhao , Jie Yu , Zhihong Sun","doi":"10.1016/j.micres.2024.127960","DOIUrl":"10.1016/j.micres.2024.127960","url":null,"abstract":"<div><div>Diabetes mellitus (DM) is a common metabolic disease and one of the diseases with the highest number of complications at present. As the disease progresses, patients will gradually develop diabetes-related cognitive decline, mild cognitive impairment (MCI) or even dementia. The occurrence of diabetes-combined cognitive impairment undoubtedly imposes a heavy burden on patients and their families. Current research suggests that risk factors such as blood glucose levels, insulin resistance, oxidative stress and neuroinflammation have an important role in the development of diabetic cognitive impairment (DCI). With the development of technology and in-depth research, the relationship between the two-way communication between the gut and the brain has been gradually revealed, and more studies have found that the gut microbiota plays an important role in the development of DCI. This review explores the feasibility of probiotics as a potential strategy to assist in the improvement of DCI and its potential mechanisms from the perspective of the factors affecting DCI.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"290 ","pages":"Article 127960"},"PeriodicalIF":6.1,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142604114","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}
Pub Date : 2024-10-31DOI: 10.1016/j.micres.2024.127943
Xiaogang Cui , Fengfeng Zhang , Hangting Meng , Tianqi Yuan , Miao Li , Dan Yuan , Xiaoxia Fan , Xiaohui Jia , Quanhong Wang , Li Xing , Changxin Wu
Exosomal microRNAs (miRNAs) in circulation were recognized as potential biomarkers for the diagnosis of multiple diseases. However, its potential as a diagnostic hallmark for tuberculosis (TB) has yet to be explored. Here, we comprehensively analyze miRNA profiles in exosomes derived from the plasma of active TB patients and healthy persons to evaluate its efficacy in TB diagnosis. Small-RNA transcriptomic profiling analysis identified a total of 14 differentially expressed miRNAs (DEmiRNAs), among which the diagnostic potential of exosomal miR-766–3p, miR-376c-3p, miR-1283, and miR-125a-5p was evident from their respective areas under the ROC curve, which were 0.8963, 0.8313, 0.8097, and 0.8050, respectively. The bioinformatics analysis and Luciferase reporter assays confirmed that the 3′-untranslated region of natural resistance-associated macrophage protein 1 (NRAMP1) mRNA was targeted by miR-766–3p. The exosomes could be internalized by the A549 cells in co-culturing experiments. Furthermore, both increased miR-766–3p and decreased NRAMP1 expression were observed in Mtb-infected A549 cells. MiR-766–3p overexpression reduced the NRAMP1 levels, but increased intracellular Mtb, suggesting that miR-766–3p may facilitate Mtb survival by targeting NRAMP1. Moreover, miR-766–3p-transfected cells exhibited increased apoptosis and reduced proliferation following Mtb infection. Taken together, circulating exosomal miR-766–3p, miR-1283, miR-125a-5p, and miR-376c-3p may serve as candidate hallmarks for TB diagnosis where the presence of miR-766–3p seems associated with the vulnerability to Mtb infection in humans and could be a new molecular target for therapeutic intervention of TB.
{"title":"Transport of miR-766–3p to A549 cells by plasma-derived exosomes and its effect on intracellular survival of Mycobacterium tuberculosis by regulating NRAMP1 expression in A549 cells","authors":"Xiaogang Cui , Fengfeng Zhang , Hangting Meng , Tianqi Yuan , Miao Li , Dan Yuan , Xiaoxia Fan , Xiaohui Jia , Quanhong Wang , Li Xing , Changxin Wu","doi":"10.1016/j.micres.2024.127943","DOIUrl":"10.1016/j.micres.2024.127943","url":null,"abstract":"<div><div>Exosomal microRNAs (miRNAs) in circulation were recognized as potential biomarkers for the diagnosis of multiple diseases. However, its potential as a diagnostic hallmark for tuberculosis (TB) has yet to be explored. Here, we comprehensively analyze miRNA profiles in exosomes derived from the plasma of active TB patients and healthy persons to evaluate its efficacy in TB diagnosis. Small-RNA transcriptomic profiling analysis identified a total of 14 differentially expressed miRNAs (DEmiRNAs), among which the diagnostic potential of exosomal miR-766–3p, miR-376c-3p, miR-1283, and miR-125a-5p was evident from their respective areas under the ROC curve, which were 0.8963, 0.8313, 0.8097, and 0.8050, respectively. The bioinformatics analysis and Luciferase reporter assays confirmed that the 3′-untranslated region of natural resistance-associated macrophage protein 1 (NRAMP1) mRNA was targeted by miR-766–3p. The exosomes could be internalized by the A549 cells in co-culturing experiments. Furthermore, both increased miR-766–3p and decreased NRAMP1 expression were observed in <em>Mtb-</em>infected A549 cells. MiR-766–3p overexpression reduced the NRAMP1 levels, but increased intracellular <em>Mtb</em>, suggesting that miR-766–3p may facilitate <em>Mtb</em> survival by targeting NRAMP1. Moreover, miR-766–3p-transfected cells exhibited increased apoptosis and reduced proliferation following <em>Mtb</em> infection. Taken together, circulating exosomal miR-766–3p, miR-1283, miR-125a-5p, and miR-376c-3p may serve as candidate hallmarks for TB diagnosis where the presence of miR-766–3p seems associated with the vulnerability to <em>Mtb</em> infection in humans and could be a new molecular target for therapeutic intervention of TB.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"290 ","pages":"Article 127943"},"PeriodicalIF":6.1,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142586194","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}
Pub Date : 2024-10-30DOI: 10.1016/j.micres.2024.127959
Magdalena Pilarczyk-Zurek , Joanna Budziaszek , Keerthanaa Nandagopal , Aleksandra Kurylek , Aleksandra Kozinska , Michal Dmowski , Izabela Sitkiewicz , Izabela Kern-Zdanowicz , Joanna Koziel
Streptococcus anginosus is considered an emerging opportunistic pathogen causing life-threatening infections, including abscesses and empyema. Noticeably, clinical data revealed that S. anginosus also constitutes an important component of polymicrobial infections. Here, we showed for the first time that S. anginosus inactivates the antibacterial potential of neutrophil extracellular traps (NETs). The process is determined by a cell wall-anchored nuclease referred to as SanA, which high expression dominates in clinical strains isolated from severe infections. Nuclease activity protects S. anginosus against the antibacterial activity of NETs, supporting at the same time the survival of coexisting highly pathogenic species of Enterobacteriales. Obtained data suggest that SanA nuclease should be recognized as a critical S. anginosus virulence factor determining severe monospecies purulent infections but also shielding other pathogens promoting the development of polymicrobial infections.
{"title":"Streptococcus anginosus orchestrates antibacterial potential of NETs facilitating survival of accompanying pathogens","authors":"Magdalena Pilarczyk-Zurek , Joanna Budziaszek , Keerthanaa Nandagopal , Aleksandra Kurylek , Aleksandra Kozinska , Michal Dmowski , Izabela Sitkiewicz , Izabela Kern-Zdanowicz , Joanna Koziel","doi":"10.1016/j.micres.2024.127959","DOIUrl":"10.1016/j.micres.2024.127959","url":null,"abstract":"<div><div><em>Streptococcus anginosus</em> is considered an emerging opportunistic pathogen causing life-threatening infections, including abscesses and empyema. Noticeably, clinical data revealed that <em>S. anginosus</em> also constitutes an important component of polymicrobial infections. Here, we showed for the first time that <em>S. anginosus</em> inactivates the antibacterial potential of neutrophil extracellular traps (NETs). The process is determined by a cell wall-anchored nuclease referred to as SanA, which high expression dominates in clinical strains isolated from severe infections. Nuclease activity protects <em>S. anginosus</em> against the antibacterial activity of NETs, supporting at the same time the survival of coexisting highly pathogenic species of <em>Enterobacteriales</em>. Obtained data suggest that SanA nuclease should be recognized as a critical <em>S. anginosus</em> virulence factor determining severe monospecies purulent infections but also shielding other pathogens promoting the development of polymicrobial infections.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"290 ","pages":"Article 127959"},"PeriodicalIF":6.1,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142569063","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}
Pub Date : 2024-10-30DOI: 10.1016/j.micres.2024.127957
Yalin Chen , Chunyu Sun , Yuxin Yan , Dongxue Jiang , Shaoqi Huangfu , Lei Tian
With an alarming increase in global greenhouse gas emissions, unstable weather conditions are significantly impacting agricultural production. Drought stress is one of the frequent consequences of climate change that affects crop growth and yield. Addressing this issue is critical to ensure stable crop productivity under drought conditions. Arbuscular mycorrhizal fungi (AMF) establish symbiotic relationships with plants and enhance their resistance to adverse conditions. Effects of arbuscular mycorrhizal associations on the rhizosphere microbiome and root transcriptome under drought conditions have not been explored. Here, we investigated the effects of AMF and drought stress on rhizosphere microorganisms and root transcriptome of maize plants grown in chernozem soil. We used high-throughput sequencing data of bacterial 16S rRNA and fungal internal transcribed spacer regions (ITS) to identify rhizosphere microorganisms. Transcriptomic data were used to assess gene expression in maize plants under different treatments. Our results show that AMF maintains the composition of maize rhizosphere microorganisms under drought stress. In particular, the bacterial and fungal phyla maintained were Actinomycetes and Ascomycota, respectively. Transcriptomic data indicated that AMF influenced gene expression in maize plants under drought stress. Under drought stress, the expression of SWEET13, CHIT3, and RPL23A was significantly higher in the presence of AMF than it was without AMF inoculation, indicating better sugar transport, reduced malondialdehyde accumulation, and improved water use efficiency in AMF-inoculated maize plants. These findings suggest that AMF can enhance the resistance of maize to moderate drought stress by stabilising plant physical traits, which may help maintain the structure of the rhizosphere microbial community. This study provides valuable theoretical insights that should aid the utilization of AMF in sustainable agricultural practices.
{"title":"Impact of arbuscular mycorrhizal fungi on maize rhizosphere microbiome stability under moderate drought conditions","authors":"Yalin Chen , Chunyu Sun , Yuxin Yan , Dongxue Jiang , Shaoqi Huangfu , Lei Tian","doi":"10.1016/j.micres.2024.127957","DOIUrl":"10.1016/j.micres.2024.127957","url":null,"abstract":"<div><div>With an alarming increase in global greenhouse gas emissions, unstable weather conditions are significantly impacting agricultural production. Drought stress is one of the frequent consequences of climate change that affects crop growth and yield. Addressing this issue is critical to ensure stable crop productivity under drought conditions. Arbuscular mycorrhizal fungi (AMF) establish symbiotic relationships with plants and enhance their resistance to adverse conditions. Effects of arbuscular mycorrhizal associations on the rhizosphere microbiome and root transcriptome under drought conditions have not been explored. Here, we investigated the effects of AMF and drought stress on rhizosphere microorganisms and root transcriptome of maize plants grown in chernozem soil. We used high-throughput sequencing data of bacterial 16S rRNA and fungal internal transcribed spacer regions (ITS) to identify rhizosphere microorganisms. Transcriptomic data were used to assess gene expression in maize plants under different treatments. Our results show that AMF maintains the composition of maize rhizosphere microorganisms under drought stress. In particular, the bacterial and fungal phyla maintained were Actinomycetes and Ascomycota, respectively. Transcriptomic data indicated that AMF influenced gene expression in maize plants under drought stress. Under drought stress, the expression of <em>SWEET13</em>, <em>CHIT3</em>, and <em>RPL23A</em> was significantly higher in the presence of AMF than it was without AMF inoculation, indicating better sugar transport, reduced malondialdehyde accumulation, and improved water use efficiency in AMF-inoculated maize plants. These findings suggest that AMF can enhance the resistance of maize to moderate drought stress by stabilising plant physical traits, which may help maintain the structure of the rhizosphere microbial community. This study provides valuable theoretical insights that should aid the utilization of AMF in sustainable agricultural practices.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"290 ","pages":"Article 127957"},"PeriodicalIF":6.1,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142561384","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}
Pub Date : 2024-10-28DOI: 10.1016/j.micres.2024.127937
Zhan-nan Yang , Yu Wang , Shi-qiong Luo
Plants recruit plant-associated microbes from soil to enhance their growth and mitigate the adverse effects of pathogen invasion on plant health. How pathogens impact the interactions of the plant-associated microbes and plant growth is poorly understood. We established S-microsystems (sterile soil inoculated with 101 bacteria isolated from humus soil with Artemisia annua, Oryza sativa or Houttuynia cordata), and N-microsystems (natural soil with these plants) to evaluate the effects of the fungus Globisporangium ultimum on plant growth and their colonizing bacterial communities (CBCs). S-microsystems and N-microsystems were inoculated with and without G. ultimum, respectively. Their seedling growth and CBCs were investigated. Plant height and root numbers in A. annua, O. sativa and H. cordata S-microsystems with G. ultimum were 34.5 % and 52.8 %, 23.1 % and 31.3 %, 102.1 % and 45.0 % higher than those without G. ultimum, respectively. The CBCs were diverse among S-microsystems of A. annua, O. sativa and H. cordata, and the CBC abundances in the three S-microsystems without G. ultimum were higher than those with G. ultimum. The relative abundances of bacterial genera Rhizobium, Pseudomonas, Brevundimonas and Cupriavidus were significantly positively related to plant growth. We determined that the CBCs in A. annua, O. sativa and H. cordata were selective and related to the plant species, and can mitigate disadvantageous influences of G. ultimum on seedling growth. The plants and their CBCs’ abundance and composition were differentially affected by G. ultimum. Our results provide evidence that CBCs promote plant growth due to dynamic changes in the composition and abundance of CBC members, which were affected by plant species and biotic factors.
{"title":"Effect of pathogen Globisporangium ultimum on plant growth and colonizing bacterial communities","authors":"Zhan-nan Yang , Yu Wang , Shi-qiong Luo","doi":"10.1016/j.micres.2024.127937","DOIUrl":"10.1016/j.micres.2024.127937","url":null,"abstract":"<div><div>Plants recruit plant-associated microbes from soil to enhance their growth and mitigate the adverse effects of pathogen invasion on plant health. How pathogens impact the interactions of the plant-associated microbes and plant growth is poorly understood. We established S-microsystems (sterile soil inoculated with 101 bacteria isolated from humus soil with <em>Artemisia annua</em>, <em>Oryza sativa</em> or <em>Houttuynia cordata</em>), and N-microsystems (natural soil with these plants) to evaluate the effects of the fungus <em>Globisporangium ultimum</em> on plant growth and their colonizing bacterial communities (CBCs). S-microsystems and N-microsystems were inoculated with and without <em>G. ultimum</em>, respectively. Their seedling growth and CBCs were investigated. Plant height and root numbers in <em>A. annua</em>, <em>O. sativa and H. cordata</em> S-microsystems with <em>G. ultimum</em> were 34.5 % and 52.8 %, 23.1 % and 31.3 %, 102.1 % and 45.0 % higher than those without <em>G. ultimum</em>, respectively. The CBCs were diverse among S-microsystems of <em>A. annua</em>, <em>O. sativa</em> and <em>H. cordata</em>, and the CBC abundances in the three S-microsystems without <em>G. ultimum</em> were higher than those with <em>G. ultimum.</em> The relative abundances of bacterial genera <em>Rhizobium</em>, <em>Pseudomonas</em>, <em>Brevundimonas</em> and <em>Cupriavidus</em> were significantly positively related to plant growth. We determined that the CBCs in <em>A. annua</em>, <em>O. sativa</em> and <em>H. cordata</em> were selective and related to the plant species, and can mitigate disadvantageous influences of <em>G. ultimum</em> on seedling growth. The plants and their CBCs’ abundance and composition were differentially affected by <em>G. ultimum.</em> Our results provide evidence that CBCs promote plant growth due to dynamic changes in the composition and abundance of CBC members, which were affected by plant species and biotic factors.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"290 ","pages":"Article 127937"},"PeriodicalIF":6.1,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142569061","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}
Pub Date : 2024-10-28DOI: 10.1016/j.micres.2024.127955
Leandro Vieira dos Santos , Thiago Neitzel , Cleiton Santos Lima , Lucas Miguel de Carvalho , Tatiani Brenelli de Lima , Jaciane Lutz Ienczak , Thamy Lívia Ribeiro Corrêa , Gonçalo Amarante Guimarães Pereira
The transition from fossil fuels dependency to embracing renewable alternatives is pivotal for mitigating greenhouse gas emissions, with biorefineries playing a central role at the forefront of this transition. As a sustainable alternative, lignocellulosic feedstocks hold great promise for biofuels and biochemicals production. However, the effective utilization of complex sugars, such as xylose, remains a significant hurdle. To address this challenge, yeasts can be engineered as microbial platforms to convert the complex sugars derived from biomass. The efficient use of xylose by XR-XDH strains still poses a significant challenge due to redox imbalance limitations, leading to the accumulation of undesirable by-products. In this study, we focused on engineering the industrial S. cerevisiae strain PE-2, known for its robustness, and compared different strategies to balance cellular redox homeostasis, guided by a genome-scale metabolic model. Flux balance analysis guided the selection of four approaches: i. decoupling NADPH regeneration from CO2 production; ii. altering XDH cofactor affinity; iii. shifting XR cofactor preference; iv. incorporating alternate phosphoketolase and acetic acid conversion pathways. A comparative time-course targeted metabolic profile was conducted to assess the redox status of xylose-fermenting cells under anaerobic conditions. The main limitations of xylose-fermenting strains were tested and the replacement of xylose reductase with a NADH-preferred XR in the LVY142 strain proved to be the most effective strategy, resulting in an increase in ethanol yield and productivity, coupled with a reduction in by-products. Comparative analysis of various genetic approaches provided valuable insights into the complexities of redox engineering, highlighting the need for tailored strategies in yeast metabolic engineering for efficient biofuels and biochemicals production from lignocellulosic feedstocks.
{"title":"Engineering cellular redox homeostasis to optimize ethanol production in xylose-fermenting Saccharomyces cerevisiae strains","authors":"Leandro Vieira dos Santos , Thiago Neitzel , Cleiton Santos Lima , Lucas Miguel de Carvalho , Tatiani Brenelli de Lima , Jaciane Lutz Ienczak , Thamy Lívia Ribeiro Corrêa , Gonçalo Amarante Guimarães Pereira","doi":"10.1016/j.micres.2024.127955","DOIUrl":"10.1016/j.micres.2024.127955","url":null,"abstract":"<div><div>The transition from fossil fuels dependency to embracing renewable alternatives is pivotal for mitigating greenhouse gas emissions, with biorefineries playing a central role at the forefront of this transition. As a sustainable alternative, lignocellulosic feedstocks hold great promise for biofuels and biochemicals production. However, the effective utilization of complex sugars, such as xylose, remains a significant hurdle. To address this challenge, yeasts can be engineered as microbial platforms to convert the complex sugars derived from biomass. The efficient use of xylose by XR-XDH strains still poses a significant challenge due to redox imbalance limitations, leading to the accumulation of undesirable by-products. In this study, we focused on engineering the industrial <em>S. cerevisiae</em> strain PE-2, known for its robustness, and compared different strategies to balance cellular redox homeostasis, guided by a genome-scale metabolic model. Flux balance analysis guided the selection of four approaches: i. decoupling NADPH regeneration from CO<sub>2</sub> production; ii. altering XDH cofactor affinity; iii. shifting XR cofactor preference; iv. incorporating alternate phosphoketolase and acetic acid conversion pathways. A comparative time-course targeted metabolic profile was conducted to assess the redox status of xylose-fermenting cells under anaerobic conditions. The main limitations of xylose-fermenting strains were tested and the replacement of xylose reductase with a NADH-preferred XR in the LVY142 strain proved to be the most effective strategy, resulting in an increase in ethanol yield and productivity, coupled with a reduction in by-products. Comparative analysis of various genetic approaches provided valuable insights into the complexities of redox engineering, highlighting the need for tailored strategies in yeast metabolic engineering for efficient biofuels and biochemicals production from lignocellulosic feedstocks.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"290 ","pages":"Article 127955"},"PeriodicalIF":6.1,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142546349","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}
Pub Date : 2024-10-28DOI: 10.1016/j.micres.2024.127942
Ayesha Ahmed, Yinglong Liu, Rizwan Khan, Pengbo He, Pengfei He, Yixin Wu, Shahzad Munir, Yueqiu He
Metabolites of plant and microbial origin have a great influence on plant-microbe interactions. Members from Bacillus subtilis are known to produce a plethora of metabolites that shape plant responses towards biotic and abiotic stresses. Similarly, endophyte B. subtilis L1–21 efficiently controls the Huanglongbing (HLB) causing pathogen: Candidatus Liberibacter asiaticus (CLas). However, the molecular mechanisms are highly elusive. Herein, our study highlights the critical role of endophyte L1–21 in planta-produced surfactin in its colonization in citrus plants and regulation of plant-microbe interactions by comparing three gene knockout mutants △srfAA-L1–21, △sfp-L1–21, and △pel-L1–21. All three mutants exhibited reduced pathogen control and colonization efficiency compared to wild-type (WT) L1–21, but knockout mutant deficient of surfactin △srfAA-L1–21 was significantly impaired in the abovementioned functions as compared to △sfp-L1–21 and △pel-L1–21. Further, △srfAA-L1–21 could not activate various metabolic pathways in citrus as WT-L1–21. Integrated metabolomic-transcriptomic analysis reveals that important secondary metabolites such as flavonoids, volatile organic compounds, and lignins were highly accumulated in citrus plants treated with WT-L1–21 as compared to △srfAA-L1–21, highlighting the role of surfactin as an elicitor of the defense system in citrus-HLB pathosystem. Interestingly, auxin-related metabolites and transcripts were also downregulated in △srfAA-L1–21 compared to WT-L1–21 showing that surfactin might also influence plant-microbe interactions through metabolic reprogramming. Further, higher enrichment of Bacilli with WT-L1–21 might corresponds to surfactin-mediated regulation of community-related behavior in Bacilli. To the best of our knowledge, this is the first study reporting the role of surfactin from Bacillus endophyte in metabolic reprogramming in citrus-HLB pathosystem and mounting defense response against CLas pathogen.
{"title":"Molecular insights from integrated metabolome-transcriptome into endophyte Bacillus subtilis L1-21 surfactin against citrus Huanglongbing","authors":"Ayesha Ahmed, Yinglong Liu, Rizwan Khan, Pengbo He, Pengfei He, Yixin Wu, Shahzad Munir, Yueqiu He","doi":"10.1016/j.micres.2024.127942","DOIUrl":"10.1016/j.micres.2024.127942","url":null,"abstract":"<div><div>Metabolites of plant and microbial origin have a great influence on plant-microbe interactions. Members from <em>Bacillus subtilis</em> are known to produce a plethora of metabolites that shape plant responses towards biotic and abiotic stresses. Similarly, endophyte <em>B. subtilis</em> L1–21 efficiently controls the Huanglongbing (HLB) causing pathogen: <em>Candidatus</em> Liberibacter asiaticus (<em>C</em>Las). However, the molecular mechanisms are highly elusive. Herein, our study highlights the critical role of endophyte L1–21 <em>in planta</em>-produced surfactin in its colonization in citrus plants and regulation of plant-microbe interactions by comparing three gene knockout mutants △<em>srfAA</em>-L1–21, △<em>sfp</em>-L1–21, and △<em>pel</em>-L1–21. All three mutants exhibited reduced pathogen control and colonization efficiency compared to wild-type (WT) L1–21, but knockout mutant deficient of surfactin △<em>srfAA</em>-L1–21 was significantly impaired in the abovementioned functions as compared to △<em>sfp</em>-L1–21 and △<em>pel</em>-L1–21. Further, △<em>srfAA</em>-L1–21 could not activate various metabolic pathways in citrus as WT-L1–21. Integrated metabolomic-transcriptomic analysis reveals that important secondary metabolites such as flavonoids, volatile organic compounds, and lignins were highly accumulated in citrus plants treated with WT-L1–21 as compared to △<em>srfAA</em>-L1–21<em>,</em> highlighting the role of surfactin as an elicitor of the defense system in citrus-HLB pathosystem. Interestingly, auxin-related metabolites and transcripts were also downregulated in △<em>srfAA</em>-L1–21 compared to WT-L1–21 showing that surfactin might also influence plant-microbe interactions through metabolic reprogramming. Further, higher enrichment of Bacilli with WT-L1–21 might corresponds to surfactin-mediated regulation of community-related behavior in Bacilli. To the best of our knowledge, this is the first study reporting the role of surfactin from <em>Bacillus</em> endophyte in metabolic reprogramming in citrus-HLB pathosystem and mounting defense response against <em>C</em>Las pathogen.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"290 ","pages":"Article 127942"},"PeriodicalIF":6.1,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142644014","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}
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