Pub Date : 2024-08-21Epub Date: 2024-07-31DOI: 10.1128/aem.01148-24
Jia-He Hung, Shi-Min Zhang, Shir-Ly Huang
Veillonella spp. are nitrate-reducing bacteria with anaerobic respiratory activity that reduce nitrate to nitrite. They are obligate anaerobic, Gram-negative cocci that ferment lactate as the main carbon source and produce short-chain fatty acids (SCFAs). Commensal Veillonella reside in the human body site where lactate level is, however, limited for Veillonella growth. In this study, nitrate was shown to promote the anaerobic growth of Veillonella in the lactate-deficient media. We aimed to investigate the underlying mechanisms and the metabolism involved in nitrate respiration. Nitrate (15 mM) was demonstrated to promote Veillonella dispar growth and viability in the tryptone-yeast extract medium containing 0.5 mM L-lactate. Metabolite and transcriptomic analyses revealed nitrate enabled V. dispar to actively utilize glutamate and aspartate from the medium and secrete tryptophan. Glutamate or aspartate was further supplemented to a medium to investigate individual catabolism during nitrate respiration. Notably, nitrate was demonstrated to elevate SCFA production in the glutamate-supplemented medium, and further increase tryptophan production in the aspartate-supplemented medium. We proposed that the increased consumption of glutamate provided reducing power for nitrate respiration and aspartate served as a substrate for fumarate formation. Both glutamate and aspartate were incorporated into the central metabolic pathways via reverse tricarboxylic acid cycle and were linked with the increased production of acetate, propionate, and tryptophan. This study provides further understanding of the promoted growth and metabolic mechanisms by commensal V. dispar utilizing nitrate and specific amino acids to adapt to the lactate-deficient environment.IMPORTANCENitrate is a pivotal ecological factor influencing microbial community and metabolism. Dietary nitrate provides health benefits including anti-diabetic and anti-hypertensive effects via microbial-derived metabolites such as nitrite. Unraveling the impacts of nitrate on the growth and metabolism of human commensal bacteria is imperative to comprehend the intricate roles of nitrate in regulating microbial metabolism, community, and human health. Veillonella are lactate-utilizing, nitrate-reducing bacteria that are frequently found in the human body site where lactate levels are low and nitrate is at millimolar levels. Here, we comprehensively described the metabolic strategies employed by V. dispar to thrive in the lactate-deficient environment using nitrate respiration and catabolism of specific amino acids. The elevated production of SCFAs and tryptophan from amino acids during nitrate respiration of V. dispar further suggested the potential roles of nitrate and Veillonella in the promotion of human health.
Veillonella 菌属是硝酸盐还原菌,具有厌氧呼吸活性,可将硝酸盐还原为亚硝酸盐。它们是必须厌氧的革兰氏阴性球菌,以乳酸盐为主要碳源进行发酵,并产生短链脂肪酸(SCFAs)。维氏菌寄生在人体部位,但人体部位的乳酸盐水平限制了维氏菌的生长。在本研究中,硝酸盐被证明能促进维氏菌在乳酸盐缺乏的培养基中厌氧生长。我们的目的是研究硝酸盐呼吸所涉及的基本机制和新陈代谢。在含有 0.5 mM L-乳酸盐的胰蛋白酶-酵母提取物培养基中,硝酸盐(15 mM)被证明能促进 Veillonella 的生长和存活。代谢物和转录组分析表明,硝酸盐能使Veillonella dispar积极利用培养基中的谷氨酸和天冬氨酸,并分泌色氨酸。进一步向培养基中添加谷氨酸或天门冬氨酸,以研究硝酸盐呼吸过程中的个体分解代谢。值得注意的是,在补充谷氨酸的培养基中,硝酸盐被证明能提高 SCFA 的产生,而在补充天门冬氨酸的培养基中,色氨酸的产生进一步增加。我们认为,谷氨酸消耗的增加为硝酸盐呼吸提供了还原力,而天冬氨酸则成为富马酸形成的底物。谷氨酸和天门冬氨酸都通过反向三羧酸循环进入中央代谢途径,并与乙酸盐、丙酸盐和色氨酸产量的增加有关。这项研究让人们进一步了解了共生菌 V. dispar 利用硝酸盐和特定氨基酸适应乳酸盐缺乏环境的促进生长和代谢机制。重要意义硝酸盐是影响微生物群落和代谢的关键生态因子。膳食硝酸盐通过微生物衍生的代谢物(如亚硝酸盐)提供健康益处,包括抗糖尿病和抗高血压作用。要理解硝酸盐在调节微生物代谢、群落和人类健康方面的复杂作用,就必须揭示硝酸盐对人类共生细菌的生长和代谢的影响。Veillonella是一种利用乳酸盐的硝酸盐还原菌,经常出现在乳酸盐水平较低而硝酸盐处于毫摩尔水平的人体部位。在这里,我们全面描述了V. dispar利用硝酸盐呼吸和特定氨基酸的分解代谢在乳酸盐缺乏的环境中茁壮成长的代谢策略。在V. dispar的硝酸盐呼吸过程中,氨基酸产生的SCFAs和色氨酸增加,这进一步说明了硝酸盐和Veillonella在促进人类健康方面的潜在作用。
{"title":"Nitrate promotes the growth and the production of short-chain fatty acids and tryptophan from commensal anaerobe <i>Veillonella dispar</i> in the lactate-deficient environment by facilitating the catabolism of glutamate and aspartate.","authors":"Jia-He Hung, Shi-Min Zhang, Shir-Ly Huang","doi":"10.1128/aem.01148-24","DOIUrl":"10.1128/aem.01148-24","url":null,"abstract":"<p><p><i>Veillonella</i> spp. are nitrate-reducing bacteria with anaerobic respiratory activity that reduce nitrate to nitrite. They are obligate anaerobic, Gram-negative cocci that ferment lactate as the main carbon source and produce short-chain fatty acids (SCFAs). Commensal <i>Veillonella</i> reside in the human body site where lactate level is, however, limited for <i>Veillonella</i> growth. In this study, nitrate was shown to promote the anaerobic growth of <i>Veillonella</i> in the lactate-deficient media. We aimed to investigate the underlying mechanisms and the metabolism involved in nitrate respiration. Nitrate (15 mM) was demonstrated to promote <i>Veillonella dispar</i> growth and viability in the tryptone-yeast extract medium containing 0.5 mM L-lactate. Metabolite and transcriptomic analyses revealed nitrate enabled <i>V. dispar</i> to actively utilize glutamate and aspartate from the medium and secrete tryptophan. Glutamate or aspartate was further supplemented to a medium to investigate individual catabolism during nitrate respiration. Notably, nitrate was demonstrated to elevate SCFA production in the glutamate-supplemented medium, and further increase tryptophan production in the aspartate-supplemented medium. We proposed that the increased consumption of glutamate provided reducing power for nitrate respiration and aspartate served as a substrate for fumarate formation. Both glutamate and aspartate were incorporated into the central metabolic pathways <i>via</i> reverse tricarboxylic acid cycle and were linked with the increased production of acetate, propionate, and tryptophan. This study provides further understanding of the promoted growth and metabolic mechanisms by commensal <i>V. dispar</i> utilizing nitrate and specific amino acids to adapt to the lactate-deficient environment.IMPORTANCENitrate is a pivotal ecological factor influencing microbial community and metabolism. Dietary nitrate provides health benefits including anti-diabetic and anti-hypertensive effects <i>via</i> microbial-derived metabolites such as nitrite. Unraveling the impacts of nitrate on the growth and metabolism of human commensal bacteria is imperative to comprehend the intricate roles of nitrate in regulating microbial metabolism, community, and human health. <i>Veillonella</i> are lactate-utilizing, nitrate-reducing bacteria that are frequently found in the human body site where lactate levels are low and nitrate is at millimolar levels. Here, we comprehensively described the metabolic strategies employed by <i>V. dispar</i> to thrive in the lactate-deficient environment using nitrate respiration and catabolism of specific amino acids. The elevated production of SCFAs and tryptophan from amino acids during nitrate respiration of <i>V. dispar</i> further suggested the potential roles of nitrate and <i>Veillonella</i> in the promotion of human health.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11337843/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141854576","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 : 2024-08-21Epub Date: 2024-07-31DOI: 10.1128/aem.00340-24
Zachary Jansen, Abdulaziz Alameri, Qiyao Wei, Devon L Kulhanek, Andrew R Gilmour, Sean Halper, Nathan D Schwalm, Ross Thyer
Soil-dwelling Actinomycetes are a diverse and ubiquitous component of the global microbiome but largely lack genetic tools comparable to those available in model species such as Escherichia coli or Pseudomonas putida, posing a fundamental barrier to their characterization and utilization as hosts for biotechnology. To address this, we have developed a modular plasmid assembly framework, along with a series of genetic control elements for the previously genetically intractable Gram-positive environmental isolate Rhodococcus ruber C208, and demonstrate conserved functionality in 11 additional environmental isolates of Rhodococcus, Nocardia, and Gordonia. This toolkit encompasses five Mycobacteriale origins of replication, five broad-host-range antibiotic resistance markers, transcriptional and translational control elements, fluorescent reporters, a tetracycline-inducible system, and a counter-selectable marker. We use this toolkit to interrogate the carotenoid biosynthesis pathway in Rhodococcus erythropolis N9T-4, a weakly carotenogenic environmental isolate and engineer higher pathway flux toward the keto-carotenoid canthaxanthin. This work establishes several new genetic tools for environmental Mycobacteriales and provides a synthetic biology framework to support the design of complex genetic circuits in these species.IMPORTANCESoil-dwelling Actinomycetes, particularly the Mycobacteriales, include both diverse new hosts for sustainable biomanufacturing and emerging opportunistic pathogens. Rhodococcus, Gordonia, and Nocardia are three abundant genera with particularly flexible metabolisms and untapped potential for natural product discovery. Among these, Rhodococcus ruber C208 was shown to degrade polyethylene; Gordonia paraffinivorans can assimilate carbon from solid hydrocarbons; and Nocardia neocaledoniensis (and many other Nocardia spp.) possesses dual isoprenoid biosynthesis pathways. Many species accumulate high levels of carotenoid pigments, indicative of highly active isoprenoid biosynthesis pathways which may be harnessed for fermentation of terpenes and other commodity isoprenoids. Modular genetic toolkits have proven valuable for both fundamental and applied research in model organisms, but such tools are lacking for most Actinomycetes. Our suite of genetic tools and DNA assembly framework were developed for broad functionality and to facilitate rapid prototyping of genetic constructs in these organisms.
{"title":"A modular toolkit for environmental <i>Rhodococcus</i>, <i>Gordonia</i>, and <i>Nocardia</i> enables complex metabolic manipulation.","authors":"Zachary Jansen, Abdulaziz Alameri, Qiyao Wei, Devon L Kulhanek, Andrew R Gilmour, Sean Halper, Nathan D Schwalm, Ross Thyer","doi":"10.1128/aem.00340-24","DOIUrl":"10.1128/aem.00340-24","url":null,"abstract":"<p><p>Soil-dwelling Actinomycetes are a diverse and ubiquitous component of the global microbiome but largely lack genetic tools comparable to those available in model species such as <i>Escherichia coli</i> or <i>Pseudomonas putida</i>, posing a fundamental barrier to their characterization and utilization as hosts for biotechnology. To address this, we have developed a modular plasmid assembly framework, along with a series of genetic control elements for the previously genetically intractable Gram-positive environmental isolate <i>Rhodococcus ruber</i> C208, and demonstrate conserved functionality in 11 additional environmental isolates of <i>Rhodococcus</i>, <i>Nocardia</i>, and <i>Gordonia</i>. This toolkit encompasses five Mycobacteriale origins of replication, five broad-host-range antibiotic resistance markers, transcriptional and translational control elements, fluorescent reporters, a tetracycline-inducible system, and a counter-selectable marker. We use this toolkit to interrogate the carotenoid biosynthesis pathway in <i>Rhodococcus erythropolis</i> N9T-4, a weakly carotenogenic environmental isolate and engineer higher pathway flux toward the keto-carotenoid canthaxanthin. This work establishes several new genetic tools for environmental Mycobacteriales and provides a synthetic biology framework to support the design of complex genetic circuits in these species.IMPORTANCESoil-dwelling Actinomycetes, particularly the Mycobacteriales, include both diverse new hosts for sustainable biomanufacturing and emerging opportunistic pathogens. <i>Rhodococcus</i>, <i>Gordonia</i>, and <i>Nocardia</i> are three abundant genera with particularly flexible metabolisms and untapped potential for natural product discovery. Among these, <i>Rhodococcus ruber</i> C208 was shown to degrade polyethylene; <i>Gordonia paraffinivorans</i> can assimilate carbon from solid hydrocarbons; and <i>Nocardia neocaledoniensis</i> (and many other <i>Nocardia</i> spp.) possesses dual isoprenoid biosynthesis pathways. Many species accumulate high levels of carotenoid pigments, indicative of highly active isoprenoid biosynthesis pathways which may be harnessed for fermentation of terpenes and other commodity isoprenoids. Modular genetic toolkits have proven valuable for both fundamental and applied research in model organisms, but such tools are lacking for most Actinomycetes. Our suite of genetic tools and DNA assembly framework were developed for broad functionality and to facilitate rapid prototyping of genetic constructs in these organisms.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11337820/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141854568","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 : 2024-08-21Epub Date: 2024-07-16DOI: 10.1128/aem.00515-24
Erick V S Motta, Tyler K de Jong, Alejandra Gage, Joseph A Edwards, Nancy A Moran
Biofilm formation is a common adaptation enabling bacteria to thrive in various environments and withstand external pressures. In the context of host-microbe interactions, biofilms play vital roles in establishing microbiomes associated with animals and plants and are used by opportunistic microbes to facilitate survival within hosts. Investigating biofilm dynamics, composition, and responses to environmental stressors is crucial for understanding microbial community assembly and biofilm regulation in health and disease. In this study, we explore in vivo colonization and in vitro biofilm formation abilities of core members of the honey bee (Apis mellifera) gut microbiota. Additionally, we assess the impact of glyphosate, a widely used herbicide with antimicrobial properties, and a glyphosate-based herbicide formulation on growth and biofilm formation in bee gut symbionts as well as in other biofilm-forming bacteria associated with diverse animals and plants. Our results demonstrate that several strains of core bee gut bacterial species can colonize the bee gut, which probably depends on their ability to form biofilms. Furthermore, glyphosate exposure elicits variable effects on bacterial growth and biofilm formation. In some instances, the effects correlate with the bacteria's ability to encode a susceptible or tolerant version of the enzyme inhibited by glyphosate in the shikimate pathway. However, in other instances, no such correlation is observed. Testing the herbicide formulation further complicates comparisons, as results often diverge from glyphosate exposure alone, suggesting that co-formulants influence bacterial growth and biofilm formation. These findings highlight the nuanced impacts of environmental stressors on microbial biofilms, with both ecological and host health-related implications.
Importance: Biofilms are essential for microbial communities to establish and thrive in diverse environments. In the honey bee gut, the core microbiota member Snodgrassella alvi forms biofilms, potentially aiding the establishment of other members and promoting interactions with the host. In this study, we show that specific strains of other core members, including Bifidobacterium, Bombilactobacillus, Gilliamella, and Lactobacillus, also form biofilms in vitro. We then examine the impact of glyphosate, a widely used herbicide that can disrupt the bee microbiota, on bacterial growth and biofilm formation. Our findings demonstrate the diverse effects of glyphosate on biofilm formation, ranging from inhibition to enhancement, reflecting observations in other beneficial or pathogenic bacteria associated with animals and plants. Thus, glyphosate exposure may influence bacterial growth and biofilm formation, potentially shaping microbial establishment on host surfaces and impacting health outcomes.
{"title":"Glyphosate effects on growth and biofilm formation in bee gut symbionts and diverse associated bacteria.","authors":"Erick V S Motta, Tyler K de Jong, Alejandra Gage, Joseph A Edwards, Nancy A Moran","doi":"10.1128/aem.00515-24","DOIUrl":"10.1128/aem.00515-24","url":null,"abstract":"<p><p>Biofilm formation is a common adaptation enabling bacteria to thrive in various environments and withstand external pressures. In the context of host-microbe interactions, biofilms play vital roles in establishing microbiomes associated with animals and plants and are used by opportunistic microbes to facilitate survival within hosts. Investigating biofilm dynamics, composition, and responses to environmental stressors is crucial for understanding microbial community assembly and biofilm regulation in health and disease. In this study, we explore <i>in vivo</i> colonization and <i>in vitro</i> biofilm formation abilities of core members of the honey bee (<i>Apis mellifera</i>) gut microbiota. Additionally, we assess the impact of glyphosate, a widely used herbicide with antimicrobial properties, and a glyphosate-based herbicide formulation on growth and biofilm formation in bee gut symbionts as well as in other biofilm-forming bacteria associated with diverse animals and plants. Our results demonstrate that several strains of core bee gut bacterial species can colonize the bee gut, which probably depends on their ability to form biofilms. Furthermore, glyphosate exposure elicits variable effects on bacterial growth and biofilm formation. In some instances, the effects correlate with the bacteria's ability to encode a susceptible or tolerant version of the enzyme inhibited by glyphosate in the shikimate pathway. However, in other instances, no such correlation is observed. Testing the herbicide formulation further complicates comparisons, as results often diverge from glyphosate exposure alone, suggesting that co-formulants influence bacterial growth and biofilm formation. These findings highlight the nuanced impacts of environmental stressors on microbial biofilms, with both ecological and host health-related implications.</p><p><strong>Importance: </strong>Biofilms are essential for microbial communities to establish and thrive in diverse environments. In the honey bee gut, the core microbiota member <i>Snodgrassella alvi</i> forms biofilms, potentially aiding the establishment of other members and promoting interactions with the host. In this study, we show that specific strains of other core members, including <i>Bifidobacterium</i>, <i>Bombilactobacillus</i>, <i>Gilliamella</i>, and <i>Lactobacillus</i>, also form biofilms <i>in vitro</i>. We then examine the impact of glyphosate, a widely used herbicide that can disrupt the bee microbiota, on bacterial growth and biofilm formation. Our findings demonstrate the diverse effects of glyphosate on biofilm formation, ranging from inhibition to enhancement, reflecting observations in other beneficial or pathogenic bacteria associated with animals and plants. Thus, glyphosate exposure may influence bacterial growth and biofilm formation, potentially shaping microbial establishment on host surfaces and impacting health outcomes.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11337805/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141619124","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 : 2024-08-21Epub Date: 2024-07-16DOI: 10.1128/aem.00292-24
Briana C Kubik, James F Holden
Various environmental factors, including H2 availability, metabolic tradeoffs, optimal growth temperature, stochasticity, and hydrology, were examined to determine if they affect microbial competition between three autotrophic thermophiles. The thiosulfate reducer Desulfurobacterium thermolithotrophum (Topt72°C) was grown in mono- and coculture separately with the methanogens Methanocaldococcus jannaschii (Topt82°C) at 72°C and Methanothermococcus thermolithotrophicus (Topt65°C) at 65°C at high and low H2 concentrations. Both methanogens showed a metabolic tradeoff shifting from high growth rate-low cell yield at high H2 concentrations to low growth rate-high cell yield at low H2 concentrations and when grown in coculture with the thiosulfate reducer. In 1:1 initial ratios, D. thermolithotrophum outcompeted both methanogens at high and low H2, no H2S was detected on low H2, and it grew with only CO2 as the electron acceptor indicating a similar metabolic tradeoff with low H2. When the initial methanogen-to-thiosulfate reducer ratio varied from 1:1 to 104:1 with high H2, D. thermolithotrophum always outcompeted M. jannaschii at 72°C. However, M. thermolithotrophicus outcompeted D. thermolithotrophum at 65°C when the ratio was 103:1. A reactive transport model that mixed pure hydrothermal fluid with cold seawater showed that hyperthermophilic methanogens dominated in systems where the residence time of the mixed fluid above 72°C was sufficiently high. With shorter residence times, thermophilic thiosulfate reducers dominated. If residence times increased with decreasing fluid temperature along the flow path, then thermophilic methanogens could dominate. Thermophilic methanogen dominance spread to previously thiosulfate-reducer-dominated conditions if the initial ratio of thermophilic methanogen-to-thiosulfate reducer increased.
Importance: The deep subsurface is the largest reservoir of microbial biomass on Earth and serves as an analog for life on the early Earth and extraterrestrial environments. Methanogenesis and sulfur reduction are among the more common chemolithoautotrophic metabolisms found in hot anoxic hydrothermal vent environments. Competition between H2-oxidizing sulfur reducers and methanogens is primarily driven by the thermodynamic favorability of redox reactions with the former outcompeting methanogens. This study demonstrated that competition between the hydrothermal vent chemolithoautotrophs Methanocaldococcus jannaschii, Methanothermococcus thermolithotrophicus, and Desulfurobacterium thermolithotrophum is also influenced by other overlapping factors such as staggered optimal growth temperatures, stochasticity, and hydrology. By modeling all a
{"title":"Non-thermodynamic factors affect competition between thermophilic chemolithoautotrophs from deep-sea hydrothermal vents.","authors":"Briana C Kubik, James F Holden","doi":"10.1128/aem.00292-24","DOIUrl":"10.1128/aem.00292-24","url":null,"abstract":"<p><p>Various environmental factors, including H<sub>2</sub> availability, metabolic tradeoffs, optimal growth temperature, stochasticity, and hydrology, were examined to determine if they affect microbial competition between three autotrophic thermophiles. The thiosulfate reducer <i>Desulfurobacterium thermolithotrophum</i> (<i>T</i><sub>opt</sub>72°C) was grown in mono- and coculture separately with the methanogens <i>Methanocaldococcus jannaschii</i> (<i>T</i><sub>opt</sub>82°C) at 72°C and <i>Methanothermococcus thermolithotrophicu</i>s (<i>T</i><sub>opt</sub>65°C) at 65°C at high and low H<sub>2</sub> concentrations. Both methanogens showed a metabolic tradeoff shifting from high growth rate-low cell yield at high H<sub>2</sub> concentrations to low growth rate-high cell yield at low H<sub>2</sub> concentrations and when grown in coculture with the thiosulfate reducer. In 1:1 initial ratios, <i>D. thermolithotrophum</i> outcompeted both methanogens at high and low H<sub>2</sub>, no H<sub>2</sub>S was detected on low H<sub>2</sub>, and it grew with only CO<sub>2</sub> as the electron acceptor indicating a similar metabolic tradeoff with low H<sub>2</sub>. When the initial methanogen-to-thiosulfate reducer ratio varied from 1:1 to 10<sup>4</sup>:1 with high H<sub>2</sub>, <i>D. thermolithotrophum</i> always outcompeted <i>M. jannaschii</i> at 72°C. However, <i>M. thermolithotrophicus</i> outcompeted <i>D. thermolithotrophum</i> at 65°C when the ratio was 10<sup>3</sup>:1. A reactive transport model that mixed pure hydrothermal fluid with cold seawater showed that hyperthermophilic methanogens dominated in systems where the residence time of the mixed fluid above 72°C was sufficiently high. With shorter residence times, thermophilic thiosulfate reducers dominated. If residence times increased with decreasing fluid temperature along the flow path, then thermophilic methanogens could dominate. Thermophilic methanogen dominance spread to previously thiosulfate-reducer-dominated conditions if the initial ratio of thermophilic methanogen-to-thiosulfate reducer increased.</p><p><strong>Importance: </strong>The deep subsurface is the largest reservoir of microbial biomass on Earth and serves as an analog for life on the early Earth and extraterrestrial environments. Methanogenesis and sulfur reduction are among the more common chemolithoautotrophic metabolisms found in hot anoxic hydrothermal vent environments. Competition between H2-oxidizing sulfur reducers and methanogens is primarily driven by the thermodynamic favorability of redox reactions with the former outcompeting methanogens. This study demonstrated that competition between the hydrothermal vent chemolithoautotrophs <i>Methanocaldococcus jannaschii</i>, <i>Methanothermococcus thermolithotrophicus</i>, and <i>Desulfurobacterium thermolithotrophum</i> is also influenced by other overlapping factors such as staggered optimal growth temperatures, stochasticity, and hydrology. By modeling all a","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11337833/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141619126","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 : 2024-08-21Epub Date: 2024-07-19DOI: 10.1128/aem.00753-24
Jin Chen, Ye Cui, Qingchen Xiao, Keqin Lin, Boyan Wang, Jing Zhou, Xiaoyu Li
The variation in the soil microbial community along the altitude gradient has been widely documented. However, the structure and function of the microbial communities distributed along the altitude gradient in the crater still need to be determined. We gathered soil specimens from different elevations within the Nushan volcano crater to bridge this knowledge gap. We investigated the microbial communities of bacteria and fungi in the soil. It is noteworthy that the microbial alpha diversity peaks in the middle of the crater. However, network analysis shows that bacterial (nodes 760 vs 613 vs 601) and fungal (nodes 328 vs 224 vs 400) communities are most stable at the bottom and top of the crater, respectively. Furthermore, the soil microbial network exhibited a decline, followed by an increase across varying altitudes. The core microorganisms displayed the highest correlation with pH and alkaline phosphatase (AP, as determined through redundancy analysis (RDA) and Mantel tests for correlation analysis. The fungal community has a higher number of core microorganisms, while the bacterial core microorganisms demonstrate greater susceptibility to environmental factors. In conclusion, we utilized Illumina sequencing techniques to assess the disparities in the structure and function of bacteria and fungi in the soil.IMPORTANCEThese findings serve as a foundation for future investigations on microbial communities present in volcanic soil.
土壤微生物群落沿海拔梯度的变化已被广泛记录。然而,火山口内沿海拔梯度分布的微生物群落的结构和功能仍有待确定。我们收集了努山火山口内不同海拔高度的土壤标本,以弥补这一知识空白。我们调查了土壤中细菌和真菌的微生物群落。值得注意的是,微生物阿尔法多样性在火山口中部达到高峰。然而,网络分析显示,细菌(节点 760 vs 613 vs 601)和真菌(节点 328 vs 224 vs 400)群落分别在火山口底部和顶部最为稳定。此外,不同海拔高度的土壤微生物网络呈现先下降后上升的趋势。通过冗余分析(RDA)和相关分析的曼特尔检验,核心微生物与 pH 值和碱性磷酸酶(AP)的相关性最高。真菌群落的核心微生物数量较多,而细菌核心微生物对环境因素的敏感性更高。总之,我们利用 Illumina 测序技术评估了土壤中细菌和真菌在结构和功能上的差异。重要意义这些发现为今后研究火山土壤中的微生物群落奠定了基础。
{"title":"Difference in microbial community structure along a gradient of crater altitude: insights from the Nushan volcano.","authors":"Jin Chen, Ye Cui, Qingchen Xiao, Keqin Lin, Boyan Wang, Jing Zhou, Xiaoyu Li","doi":"10.1128/aem.00753-24","DOIUrl":"10.1128/aem.00753-24","url":null,"abstract":"<p><p>The variation in the soil microbial community along the altitude gradient has been widely documented. However, the structure and function of the microbial communities distributed along the altitude gradient in the crater still need to be determined. We gathered soil specimens from different elevations within the Nushan volcano crater to bridge this knowledge gap. We investigated the microbial communities of bacteria and fungi in the soil. It is noteworthy that the microbial alpha diversity peaks in the middle of the crater. However, network analysis shows that bacterial (nodes 760 vs 613 vs 601) and fungal (nodes 328 vs 224 vs 400) communities are most stable at the bottom and top of the crater, respectively. Furthermore, the soil microbial network exhibited a decline, followed by an increase across varying altitudes. The core microorganisms displayed the highest correlation with pH and alkaline phosphatase (AP, as determined through redundancy analysis (RDA) and Mantel tests for correlation analysis. The fungal community has a higher number of core microorganisms, while the bacterial core microorganisms demonstrate greater susceptibility to environmental factors. In conclusion, we utilized Illumina sequencing techniques to assess the disparities in the structure and function of bacteria and fungi in the soil.IMPORTANCEThese findings serve as a foundation for future investigations on microbial communities present in volcanic soil.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11337807/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141722915","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Hyperosmotic stress tolerance is crucial for Saccharomyces cerevisiae in producing value-added products from renewable feedstock. The limited understanding of its tolerance mechanism has impeded the application of these microbial cell factories. Previous studies have shown that Med3 plays a role in hyperosmotic stress in S. cerevisiae. However, the specific function of Med3 in hyperosmotic stress tolerance remains unclear. In this study, we showed that the deletion of the mediator Med3 impairs S. cerevisiae growth under hyperosmotic stress. Phenotypic analyses and yeast two-hybrid assays revealed that Med3 interacts with the transcription factor Stb5 to regulate the expression of the genes gnd1 and ald6, which are involved in NADPH production under hyperosmotic stress conditions. The deletion of med3 resulted in a decrease in intracellular NADPH content, leading to increased oxidative stress and elevated levels of intracellular reactive oxygen species under hyperosmotic stress, thereby impacting bud formation. These findings highlight the significant role of Med3 as a regulator in maintaining NADPH generation and redox homeostasis in S. cerevisiae during hyperosmotic stress.IMPORTANCEHyperosmotic stress tolerance in the host strain is a significant challenge for fermentation performance in industrial production. In this study, we showed that the S. cerevisiae mediator Med3 is essential for yeast growth under hyperosmotic conditions. Med3 interacts with the transcription factor Stb5 to regulate the expression of genes involved in the NADPH-generation system during hyperosmotic stress. Adequate NADPH ensures the timely removal of excess reactive oxygen species and supports bud formation under these conditions. This work highlights the crucial role of Med3 as a regulator in maintaining NADPH generation and redox homeostasis in S. cerevisiae during hyperosmotic stress.
{"title":"Med3-mediated NADPH generation to help <i>Saccharomyces cerevisiae</i> tolerate hyperosmotic stress.","authors":"Shuo Hou, Cong Gao, Jia Liu, Xiulai Chen, Wanqing Wei, Wei Song, Guipeng Hu, Xiaomin Li, Jing Wu, Liming Liu","doi":"10.1128/aem.00968-24","DOIUrl":"10.1128/aem.00968-24","url":null,"abstract":"<p><p>Hyperosmotic stress tolerance is crucial for <i>Saccharomyces cerevisiae</i> in producing value-added products from renewable feedstock. The limited understanding of its tolerance mechanism has impeded the application of these microbial cell factories. Previous studies have shown that Med3 plays a role in hyperosmotic stress in <i>S. cerevisiae</i>. However, the specific function of Med3 in hyperosmotic stress tolerance remains unclear. In this study, we showed that the deletion of the mediator Med3 impairs <i>S. cerevisiae</i> growth under hyperosmotic stress. Phenotypic analyses and yeast two-hybrid assays revealed that Med3 interacts with the transcription factor Stb5 to regulate the expression of the genes <i>gnd1</i> and <i>ald6</i>, which are involved in NADPH production under hyperosmotic stress conditions. The deletion of <i>med3</i> resulted in a decrease in intracellular NADPH content, leading to increased oxidative stress and elevated levels of intracellular reactive oxygen species under hyperosmotic stress, thereby impacting bud formation. These findings highlight the significant role of Med3 as a regulator in maintaining NADPH generation and redox homeostasis in <i>S. cerevisiae</i> during hyperosmotic stress.IMPORTANCEHyperosmotic stress tolerance in the host strain is a significant challenge for fermentation performance in industrial production. In this study, we showed that the <i>S. cerevisiae</i> mediator Med3 is essential for yeast growth under hyperosmotic conditions. Med3 interacts with the transcription factor Stb5 to regulate the expression of genes involved in the NADPH-generation system during hyperosmotic stress. Adequate NADPH ensures the timely removal of excess reactive oxygen species and supports bud formation under these conditions. This work highlights the crucial role of Med3 as a regulator in maintaining NADPH generation and redox homeostasis in <i>S. cerevisiae</i> during hyperosmotic stress.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11337799/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141854575","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Valerie Intorcia, Rosa L Sava, Grace P Schroeder, Michael J Gebhardt
The continued emergence of antibiotic resistance among bacterial pathogens remains a significant challenge. Indeed, the enhanced antibiotic resistance profiles of contemporary pathogens often restrict the number of suitable molecular tools that are available. We have constructed a series of plasmids that confer resistance to two infrequently used antibiotics with variants of each plasmid backbone incorporating several regulatory control systems. The regulatory systems include both commonly used systems based on the lac- and arabinose-controlled promoters found in Escherichia coli, as well as less frequently used systems that respond to tetracycline/anhydrotetracycline and toluic acid. As a test case, we demonstrate the utility of these plasmids for regulated and tunable gene expression in a multidrug-resistant (MDR) isolate of Acinetobacter baumannii, strain AB5075-UW. The plasmids include derivatives of a freely replicating, broad-host-range plasmid allowing for inducible gene expression as well as a set of vectors for introducing genetic material at the highly conserved Tn7-attachment site. We also modified a set of CRISPR-interference plasmids for use in MDR organisms, thus allowing researchers to more readily interrogate essential genes in currently circulating clinical isolates. These tools will enhance molecular genetic analyses of bacterial pathogens in situations where existing plasmids cannot be used due to their antibiotic resistance determinants or lack of suitable regulatory control systems.
Importance: Clinical isolates of bacterial pathogens often harbor resistance to multiple antibiotics, with Acinetobacter baumannii being a prime example. The drug-resistance phenotypes associated with these pathogens represent a significant hurdle to researchers who wish to study modern isolates due to the limited availability of plasmid tools. Here, we present a series of freely replicating and Tn7-insertion vectors that rely on selectable markers to less frequently encountered antibiotics, apramycin, and hygromycin. We demonstrate the utility of these plasmid tools through a variety of experiments looking at a multidrug-resistant strain of A. baumannii, strain AB5075. Strain AB5075 is an established model strain for present-day A. baumannii, due in part to its genetic tractability and because it is a representative isolate of the globally disseminated multidrug-resistant clade of A. baumannii, global clone 1. In addition to the drug-selection markers facilitating use in strains resistant to more commonly used antibiotics, the vectors allow for controllable expression driven by several regulatory systems, including isopropyl β-D-1-thiogalactopyranoside (IPTG), arabinose, anhydrotetracycline, and toluic acid.
{"title":"A series of vectors for inducible gene expression in multidrug-resistant <i>Acinetobacter baumannii</i>.","authors":"Valerie Intorcia, Rosa L Sava, Grace P Schroeder, Michael J Gebhardt","doi":"10.1128/aem.00474-24","DOIUrl":"https://doi.org/10.1128/aem.00474-24","url":null,"abstract":"<p><p>The continued emergence of antibiotic resistance among bacterial pathogens remains a significant challenge. Indeed, the enhanced antibiotic resistance profiles of contemporary pathogens often restrict the number of suitable molecular tools that are available. We have constructed a series of plasmids that confer resistance to two infrequently used antibiotics with variants of each plasmid backbone incorporating several regulatory control systems. The regulatory systems include both commonly used systems based on the <i>lac-</i> and arabinose-controlled promoters found in <i>Escherichia coli</i>, as well as less frequently used systems that respond to tetracycline/anhydrotetracycline and toluic acid. As a test case, we demonstrate the utility of these plasmids for regulated and tunable gene expression in a multidrug-resistant (MDR) isolate of <i>Acinetobacter baumannii</i>, strain AB5075-UW. The plasmids include derivatives of a freely replicating, broad-host-range plasmid allowing for inducible gene expression as well as a set of vectors for introducing genetic material at the highly conserved Tn7-attachment site. We also modified a set of CRISPR-interference plasmids for use in MDR organisms, thus allowing researchers to more readily interrogate essential genes in currently circulating clinical isolates. These tools will enhance molecular genetic analyses of bacterial pathogens in situations where existing plasmids cannot be used due to their antibiotic resistance determinants or lack of suitable regulatory control systems.</p><p><strong>Importance: </strong>Clinical isolates of bacterial pathogens often harbor resistance to multiple antibiotics, with <i>Acinetobacter baumannii</i> being a prime example. The drug-resistance phenotypes associated with these pathogens represent a significant hurdle to researchers who wish to study modern isolates due to the limited availability of plasmid tools. Here, we present a series of freely replicating and Tn7-insertion vectors that rely on selectable markers to less frequently encountered antibiotics, apramycin, and hygromycin. We demonstrate the utility of these plasmid tools through a variety of experiments looking at a multidrug-resistant strain of <i>A. baumannii</i>, strain AB5075. Strain AB5075 is an established model strain for present-day <i>A. baumannii</i>, due in part to its genetic tractability and because it is a representative isolate of the globally disseminated multidrug-resistant clade of <i>A. baumannii</i>, global clone 1. In addition to the drug-selection markers facilitating use in strains resistant to more commonly used antibiotics, the vectors allow for controllable expression driven by several regulatory systems, including isopropyl β-D-1-thiogalactopyranoside (IPTG), arabinose, anhydrotetracycline, and toluic acid.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142003455","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Considering an ever-growing global population, which hit 8 billion people in the fall of 2022, it is essential to find solutions to avoid croplands competition between human food and animal feed. Agricultural co-products such as soybean meals have become important components of the circular economy thanks to their use in animal feed. Their implementation was made possible by the addition of exogenous enzymes in the diet of monogastric animals, especially fungal carbohydrate-active enzymes (CAZymes). Here, we describe a time-course production and analysis of Aspergillus terreus secretomes for the identification of CAZymes able to enhance the digestibility of soybean meals. Functional assays revealed that the release of nutrients and the degradation of pectins in soybean meals can be tightly interconnected. Using a comparative proteomics approach, we identified several fungal pectin-degrading enzymes leading to increased assimilable nutrients in the soluble fraction of soybean meals. Our results reinforce the importance of deconstructing pectic polysaccharides in feedstuffs and contribute to sharpen our understanding of the fungal enzymatic interplays involved in pectin hydrolysis.IMPORTANCEIn the present study, we developed a strategy to identify the key fungal enzymatic activities involved in the improvement of soybean meal (SBM) digestibility. Our data unravel the importance of pectin degradation for the release of nutrients from SBM and provide some insights regarding the degradation of rhamnogalacturonan-I (RG-I) by ascomycetes. Indeed, the hydrolysis of pectins and RG-I by human microbiota is well documented in the literature, but our knowledge of the fungal CAZymes at play for the degradation of soybean pectins remains hitherto underexplored. Due to its wide use in animal feed, improving the digestibility of SBM by enzymatic treatments is a current challenge for feed additive suppliers. Since non-starch polysaccharides and pectins have often been reported for their anti-nutritional role in SBM, we believe this study will provide new avenues toward the improvement of enzymatic cocktails for animal nutrition and health.
{"title":"A time-course analysis of <i>Aspergillus terreus</i> secretomes reveals the importance of pectin-degrading enzymes to increase the digestibility of soybean meal.","authors":"Lauriane Plouhinec, Estelle Bonnin, Mélodie Kielbasa, Jean Armengaud, Virginie Neugnot, Jean-Guy Berrin, Mickael Lafond","doi":"10.1128/aem.02153-23","DOIUrl":"https://doi.org/10.1128/aem.02153-23","url":null,"abstract":"<p><p>Considering an ever-growing global population, which hit 8 billion people in the fall of 2022, it is essential to find solutions to avoid croplands competition between human food and animal feed. Agricultural co-products such as soybean meals have become important components of the circular economy thanks to their use in animal feed. Their implementation was made possible by the addition of exogenous enzymes in the diet of monogastric animals, especially fungal carbohydrate-active enzymes (CAZymes). Here, we describe a time-course production and analysis of <i>Aspergillus terreus</i> secretomes for the identification of CAZymes able to enhance the digestibility of soybean meals. Functional assays revealed that the release of nutrients and the degradation of pectins in soybean meals can be tightly interconnected. Using a comparative proteomics approach, we identified several fungal pectin-degrading enzymes leading to increased assimilable nutrients in the soluble fraction of soybean meals. Our results reinforce the importance of deconstructing pectic polysaccharides in feedstuffs and contribute to sharpen our understanding of the fungal enzymatic interplays involved in pectin hydrolysis.IMPORTANCEIn the present study, we developed a strategy to identify the key fungal enzymatic activities involved in the improvement of soybean meal (SBM) digestibility. Our data unravel the importance of pectin degradation for the release of nutrients from SBM and provide some insights regarding the degradation of rhamnogalacturonan-I (RG-I) by ascomycetes. Indeed, the hydrolysis of pectins and RG-I by human microbiota is well documented in the literature, but our knowledge of the fungal CAZymes at play for the degradation of soybean pectins remains hitherto underexplored. Due to its wide use in animal feed, improving the digestibility of SBM by enzymatic treatments is a current challenge for feed additive suppliers. Since non-starch polysaccharides and pectins have often been reported for their anti-nutritional role in SBM, we believe this study will provide new avenues toward the improvement of enzymatic cocktails for animal nutrition and health.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142003456","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Tahina Onina Ranaivoarisoa, Wei Bai, Rengasamy Karthikeyan, Hope Steele, Miriam Silberman, Jennifer Olabode, Eric Conners, Brian Gallagher, Arpita Bose
With the rising demand for sustainable renewable resources, microorganisms capable of producing bioproducts such as bioplastics are attractive. While many bioproduction systems are well-studied in model organisms, investigating non-model organisms is essential to expand the field and utilize metabolically versatile strains. This investigation centers on Rhodopseudomonas palustris TIE-1, a purple non-sulfur bacterium capable of producing bioplastics. To increase bioplastic production, genes encoding the putative regulatory protein PhaR and the depolymerase PhaZ of the polyhydroxyalkanoate (PHA) biosynthesis pathway were deleted. Genes associated with pathways that might compete with PHA production, specifically those linked to glycogen production and nitrogen fixation, were deleted. Additionally, RuBisCO form I and II genes were integrated into TIE-1's genome by a phage integration system, developed in this study. Our results show that deletion of phaR increases PHA production when TIE-1 is grown photoheterotrophically with butyrate and ammonium chloride (NH4Cl). Mutants unable to produce glycogen or fix nitrogen show increased PHA production under photoautotrophic growth with hydrogen and NH4Cl. The most significant increase in PHA production was observed when RuBisCO form I and form I & II genes were overexpressed, five times under photoheterotrophy with butyrate, two times with hydrogen and NH4Cl, and two times under photoelectrotrophic growth with N2 . In summary, inserting copies of RuBisCO genes into the TIE-1 genome is a more effective strategy than deleting competing pathways to increase PHA production in TIE-1. The successful use of the phage integration system opens numerous opportunities for synthetic biology in TIE-1.IMPORTANCEOur planet has been burdened by pollution resulting from the extensive use of petroleum-derived plastics for the last few decades. Since the discovery of biodegradable plastic alternatives, concerted efforts have been made to enhance their bioproduction. The versatile microorganism Rhodopseudomonas palustris TIE-1 (TIE-1) stands out as a promising candidate for bioplastic synthesis, owing to its ability to use multiple electron sources, fix the greenhouse gas CO2, and use light as an energy source. Two categories of strains were meticulously designed from the TIE-1 wild-type to augment the production of polyhydroxyalkanoate (PHA), one such bioplastic produced. The first group includes mutants carrying a deletion of the phaR or phaZ genes in the PHA pathway, and those lacking potential competitive carbon and energy sinks to the PHA pathway (namely, glycogen biosynthesis and nitrogen fixation). The second group comprises TIE-1 strains that overexpress RuBisCO form I or form I & II genes inserted via a phage integration system. By studying numerous metabolic mutants and overexpression strains, we conclude that genetic mod
{"title":"Overexpression of RuBisCO form I and II genes in <i>Rhodopseudomonas palustris</i> TIE-1 augments polyhydroxyalkanoate production heterotrophically and autotrophically.","authors":"Tahina Onina Ranaivoarisoa, Wei Bai, Rengasamy Karthikeyan, Hope Steele, Miriam Silberman, Jennifer Olabode, Eric Conners, Brian Gallagher, Arpita Bose","doi":"10.1128/aem.01438-24","DOIUrl":"https://doi.org/10.1128/aem.01438-24","url":null,"abstract":"<p><p>With the rising demand for sustainable renewable resources, microorganisms capable of producing bioproducts such as bioplastics are attractive. While many bioproduction systems are well-studied in model organisms, investigating non-model organisms is essential to expand the field and utilize metabolically versatile strains. This investigation centers on <i>Rhodopseudomonas palustris</i> TIE-1, a purple non-sulfur bacterium capable of producing bioplastics. To increase bioplastic production, genes encoding the putative regulatory protein PhaR and the depolymerase PhaZ of the polyhydroxyalkanoate (PHA) biosynthesis pathway were deleted. Genes associated with pathways that might compete with PHA production, specifically those linked to glycogen production and nitrogen fixation, were deleted. Additionally, RuBisCO form I and II genes were integrated into TIE-1's genome by a phage integration system, developed in this study. Our results show that deletion of <i>phaR</i> increases PHA production when TIE-1 is grown photoheterotrophically with butyrate and ammonium chloride (NH<sub>4</sub>Cl). Mutants unable to produce glycogen or fix nitrogen show increased PHA production under photoautotrophic growth with hydrogen and NH<sub>4</sub>Cl. The most significant increase in PHA production was observed when RuBisCO form I and form I & II genes were overexpressed, five times under photoheterotrophy with butyrate, two times with hydrogen and NH<sub>4</sub>Cl, and two times under photoelectrotrophic growth with N<sub>2</sub> . In summary, inserting copies of RuBisCO genes into the TIE-1 genome is a more effective strategy than deleting competing pathways to increase PHA production in TIE-1. The successful use of the phage integration system opens numerous opportunities for synthetic biology in TIE-1.IMPORTANCEOur planet has been burdened by pollution resulting from the extensive use of petroleum-derived plastics for the last few decades. Since the discovery of biodegradable plastic alternatives, concerted efforts have been made to enhance their bioproduction. The versatile microorganism <i>Rhodopseudomonas palustris</i> TIE-1 (TIE-1) stands out as a promising candidate for bioplastic synthesis, owing to its ability to use multiple electron sources, fix the greenhouse gas CO<sub>2</sub>, and use light as an energy source. Two categories of strains were meticulously designed from the TIE-1 wild-type to augment the production of polyhydroxyalkanoate (PHA), one such bioplastic produced. The first group includes mutants carrying a deletion of the <i>phaR</i> or <i>phaZ</i> genes in the PHA pathway, and those lacking potential competitive carbon and energy sinks to the PHA pathway (namely, glycogen biosynthesis and nitrogen fixation). The second group comprises TIE-1 strains that overexpress RuBisCO form I or form I & II genes inserted via a phage integration system. By studying numerous metabolic mutants and overexpression strains, we conclude that genetic mod","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142003457","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Halophilic bacteria have adapted to survive in high-salinity environments by accumulating amino acids and their derivatives as organic osmolytes. L-Proline (Pro) is one such osmolyte that is also being used as a feed stimulant in the aquaculture industry. Halomonas elongata OUT30018 is a moderately halophilic bacterium that accumulates ectoine (Ect), but not Pro, as an osmolyte. Due to its ability to utilize diverse biomass-derived carbon and nitrogen sources for growth, H. elongata OUT30018 is used in this work to create a strain that overproduces Pro, which could be used as a sustainable Pro-rich feed additive. To achieve this, we replaced the coding region of H. elongata OUT30018's Ect biosynthetic operon with the artificial self-cloned proBm1AC gene cluster that encodes the Pro biosynthetic enzymes: feedback-inhibition insensitive mutant γ-glutamate kinase (γ-GKD118N/D119N), γ-glutamyl phosphate reductase, and pyrroline-5-carboxylate reductase. Additionally, the putA gene, which encodes the key enzyme of Pro catabolism, was deleted from the genome to generate H. elongata HN6. While the Ect-deficient H. elongata KA1 could not grow in minimal media containing more than 4% NaCl, H. elongata HN6 thrived in the medium containing 8% NaCl by accumulating Pro in the cell instead of Ect, reaching a concentration of 353.1 ± 40.5 µmol/g cell fresh weight, comparable to the Ect accumulated in H. elongata OUT30018 in response to salt stress. With its genetic background, H. elongata HN6 has the potential to be developed into a Pro-rich cell factory for upcycling biomass waste into single-cell feed additives, contributing to a more sustainable aquaculture industry.IMPORTANCEWe report here the evidence for de novo biosynthesis of Pro to be used as a major osmolyte in an ectoine-deficient Halomonas elongata. Remarkably, the concentration of Pro accumulated in H. elongata HN6 (∆ectABC::mCherry-proBm1AC ∆putA) is comparable to that of ectoine accumulated in H. elongata OUT30018 in response to high-salinity stress. We also found that among the two γ-glutamate kinase mutants (γ-GKD118N/D119N and γ-GKD154A/E155A) designed to resemble the two known Escherichia coli feedback-inhibition insensitive γ-GKD107N and γ-GKE143A, the γ-GKD118N/D119N mutant is the only one that became insensitive to feedback inhibition by Pro in H. elongata. As Pro is one of the essential feed additives for the poultry and aquaculture industries, the genetic makeup of the engineered H. elongata HN6 would allow for the sustainable upcycling of high-salinity waste biomass into a Pro-rich single-cell eco-feed.
嗜卤细菌通过积累氨基酸及其衍生物作为有机渗透溶质,适应在高盐度环境中生存。L-脯氨酸(Pro)就是这样一种渗透溶质,在水产养殖业中也被用作饲料刺激剂。Halomonas elongata OUT30018 是一种中度嗜卤细菌,可积累外氨酸(Ect)作为渗透溶质,但不能积累 Pro 作为渗透溶质。由于 elongata OUT30018 能够利用多种生物质衍生的碳源和氮源进行生长,因此本研究利用它来创造一种过量生产 Pro 的菌株,这种菌株可用作富含 Pro 的可持续饲料添加剂。为此,我们用人工自克隆的 proBm1AC 基因簇取代了 H. elongata OUT30018 的 Ect 生物合成操作子的编码区,该基因簇编码 Pro 生物合成酶:反馈抑制不敏感突变体γ-谷氨酸激酶(γ-GKD118N/D119N)、γ-谷氨酰磷酸还原酶和吡咯啉-5-羧酸还原酶。此外,还从基因组中删除了编码 Pro 分解代谢关键酶的 putA 基因,从而产生了 H. elongata HN6。Ect 缺陷的 H. elongata KA1 无法在含超过 4% NaCl 的最小培养基中生长,而 H. elongata HN6 则通过在细胞中积累 Pro 而不是 Ect 在含 8% NaCl 的培养基中茁壮成长,其浓度达到 353.1 ± 40.5 µmol/g 细胞鲜重,与 H. elongata OUT30018 在应对盐胁迫时积累的 Ect 相当。在其遗传背景下,H. elongata HN6 有潜力发展成为一个富含 Pro 的细胞工厂,将生物质废物循环利用为单细胞饲料添加剂,从而为更可持续的水产养殖业做出贡献。值得注意的是,H. elongata HN6(ΔectABC::mCherry-proBm1AC ΔputA)中积累的 Pro 浓度与 H. elongata OUT30018 在高盐度胁迫下积累的外氨酸浓度相当。我们还发现,在两个γ-谷氨酸激酶突变体(γ-GKD118N/D119N和γ-GKD154A/E155A)中,只有γ-GKD118N/D119N突变体对Pro的反馈抑制不敏感。由于Pro是家禽和水产养殖业的重要饲料添加剂之一,因此工程化的H. elongata HN6的基因组成可将高盐度废弃生物质可持续地循环利用为富含Pro的单细胞生态饲料。
{"title":"Metabolic pathway engineering of high-salinity-induced overproduction of L-proline improves high-salinity stress tolerance of an ectoine-deficient <i>Halomonas elongata</i>.","authors":"Huynh Cong Khanh, Pulla Kaothien-Nakayama, Ziyan Zou, Hideki Nakayama","doi":"10.1128/aem.01195-24","DOIUrl":"https://doi.org/10.1128/aem.01195-24","url":null,"abstract":"<p><p>Halophilic bacteria have adapted to survive in high-salinity environments by accumulating amino acids and their derivatives as organic osmolytes. L-Proline (Pro) is one such osmolyte that is also being used as a feed stimulant in the aquaculture industry. <i>Halomonas elongata</i> OUT30018 is a moderately halophilic bacterium that accumulates ectoine (Ect), but not Pro, as an osmolyte. Due to its ability to utilize diverse biomass-derived carbon and nitrogen sources for growth, <i>H. elongata</i> OUT30018 is used in this work to create a strain that overproduces Pro, which could be used as a sustainable Pro-rich feed additive. To achieve this, we replaced the coding region of <i>H. elongata</i> OUT30018's Ect biosynthetic operon with the artificial self-cloned <i>proB<sub>m1</sub>AC</i> gene cluster that encodes the Pro biosynthetic enzymes: feedback-inhibition insensitive mutant γ-glutamate kinase (γ-GK<sup>D118N/D119N</sup>), γ-glutamyl phosphate reductase, and pyrroline-5-carboxylate reductase. Additionally, the <i>putA</i> gene, which encodes the key enzyme of Pro catabolism, was deleted from the genome to generate <i>H. elongata</i> HN6. While the Ect-deficient <i>H. elongata</i> KA1 could not grow in minimal media containing more than 4% NaCl, <i>H. elongata</i> HN6 thrived in the medium containing 8% NaCl by accumulating Pro in the cell instead of Ect, reaching a concentration of 353.1 ± 40.5 µmol/g cell fresh weight, comparable to the Ect accumulated in <i>H. elongata</i> OUT30018 in response to salt stress. With its genetic background, <i>H. elongata</i> HN6 has the potential to be developed into a Pro-rich cell factory for upcycling biomass waste into single-cell feed additives, contributing to a more sustainable aquaculture industry.IMPORTANCEWe report here the evidence for <i>de novo</i> biosynthesis of Pro to be used as a major osmolyte in an ectoine-deficient <i>Halomonas elongata</i>. Remarkably, the concentration of Pro accumulated in <i>H. elongata</i> HN6 (<i>∆ectABC::mCherry-proB<sub>m1</sub>AC ∆putA</i>) is comparable to that of ectoine accumulated in <i>H. elongata</i> OUT30018 in response to high-salinity stress. We also found that among the two γ-glutamate kinase mutants (γ-GK<sup>D118N/D119N</sup> and γ-GK<sup>D154A/E155A</sup>) designed to resemble the two known <i>Escherichia coli</i> feedback-inhibition insensitive γ-GK<sup>D107N</sup> and γ-GK<sup>E143A</sup>, the γ-GK<sup>D118N/D119N</sup> mutant is the only one that became insensitive to feedback inhibition by Pro in <i>H. elongata</i>. As Pro is one of the essential feed additives for the poultry and aquaculture industries, the genetic makeup of the engineered <i>H. elongata</i> HN6 would allow for the sustainable upcycling of high-salinity waste biomass into a Pro-rich single-cell eco-feed.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141999252","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}