International Biodeterioration & Biodegradation最新文献_第5页

Ethiprole biodegradation by Pseudomonas sp. NC1: Insights into the mechanisms and pathways

IF 4.1 2区环境科学与生态学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

International Biodeterioration & Biodegradation

Pub Date : 2025-02-01 DOI: 10.1016/j.ibiod.2024.105985

Wenjie Wei, Yingying Wu, Zekun Sha, Zhiqiang Lu, Minghua Wang

Ethiprole is a widely used phenylpyrazole pesticide; however, microorganism-mediated degradation of ethiprole has not been reported. In this study, we isolated and identified a new and efficient strain, NC1, of Pseudomonas putida, using morphological, physiological, biochemical, and molecular methods. The strain, identified as Pseudomonas putida, utilizes ethiprole as a carbon source. We optimized the conditions for ethiprole degradation mediated by strain NC1 using the response surface method. Under optimal conditions (25 °C, pH 9, and 0.5% inoculation) we achieved a degradation rate of 79.7% within 24 h for a 50 mg/L ethiprole solution. A new ethiprole degradation pathway is proposed based on the main degradation products. The key oxidoreductase from the glucose–methanol–choline family, GmcF, involved in ethiprole degradation was identified through molecular cloning, and the degradation of other phenylimidazole insecticides by the new strain was verified using molecular docking. Additionally, we elucidated the mechanism underlying NC1 strain-mediated ethiprole degradation. We also examined the potential of the NC1 strain for the bioremediation of ethiprole-contaminated lettuce plants and soil. By optimizing this method, strain NC1 degraded 12.1% of 30 mg/L ethiprole in soil over 7 days. The half-life of ethiprole in treated lettuce plants with strain NC1 was reduced by 37.7% compared to the control group, indicating a significant effect of exogenous microorganisms on the elimination of ethiprole in lettuce plants. This study offers significant insights into the degradation pathways and mechanisms of ethiprole biodegradation and provided the basis for bioremediation of ethiprole.

{"title":"Ethiprole biodegradation by Pseudomonas sp. NC1: Insights into the mechanisms and pathways","authors":"Wenjie Wei, Yingying Wu, Zekun Sha, Zhiqiang Lu, Minghua Wang","doi":"10.1016/j.ibiod.2024.105985","DOIUrl":"10.1016/j.ibiod.2024.105985","url":null,"abstract":"<div><div>Ethiprole is a widely used phenylpyrazole pesticide; however, microorganism-mediated degradation of ethiprole has not been reported. In this study, we isolated and identified a new and efficient strain, NC1, of <em>Pseudomonas putida</em>, using morphological, physiological, biochemical, and molecular methods. The strain, identified as <em>Pseudomonas putida</em>, utilizes ethiprole as a carbon source. We optimized the conditions for ethiprole degradation mediated by strain NC1 using the response surface method. Under optimal conditions (25 °C, pH 9, and 0.5% inoculation) we achieved a degradation rate of 79.7% within 24 h for a 50 mg/L ethiprole solution. A new ethiprole degradation pathway is proposed based on the main degradation products. The key oxidoreductase from the glucose–methanol–choline family, GmcF, involved in ethiprole degradation was identified through molecular cloning, and the degradation of other phenylimidazole insecticides by the new strain was verified using molecular docking. Additionally, we elucidated the mechanism underlying NC1 strain-mediated ethiprole degradation. We also examined the potential of the NC1 strain for the bioremediation of ethiprole-contaminated lettuce plants and soil. By optimizing this method, strain NC1 degraded 12.1% of 30 mg/L ethiprole in soil over 7 days. The half-life of ethiprole in treated lettuce plants with strain NC1 was reduced by 37.7% compared to the control group, indicating a significant effect of exogenous microorganisms on the elimination of ethiprole in lettuce plants. This study offers significant insights into the degradation pathways and mechanisms of ethiprole biodegradation and provided the basis for bioremediation of ethiprole.</div></div>","PeriodicalId":13643,"journal":{"name":"International Biodeterioration & Biodegradation","volume":"198 ","pages":"Article 105985"},"PeriodicalIF":4.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143164689","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Molecular docking simulation of anaerobic biodegradation pathways of petroleum hydrocarbons in oil reservoir

IF 4.1 2区环境科学与生态学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

International Biodeterioration & Biodegradation

Pub Date : 2025-02-01 DOI: 10.1016/j.ibiod.2024.105972

Shiqi Wang , Qichao Xie , Haitong Yang , Xiaodong Chen , Wen Liu , Congcong Li , Shuoliang Wang

In-depth study of the anaerobic biodegradation mechanism of petroleum hydrocarbons is of great significance for microbial oil recovery and bioremediation. This study retrieved microorganisms with genes for anaerobic hydrocarbon degradation from the PATRIC and NCBI databases, and compiled taxonomic information of core microorganisms containing multiple functional genes. Molecular docking simulations were conducted on 11 enzymes involved in the initial degradation pathways, such as fumarate addition reaction, anaerobic hydroxylation, and anaerobic carboxylation. The simulations revealed the petroleum hydrocarbon binding energy, binding affinity, and binding site within the enzyme cavity. The results indicated that the core microbial bacterial lineages with anaerobic degradation functional genes mainly included Bacillota and Proteobacteria. Enzymes in the same initial degradation pathway continuously catalysed the anaerobic degradation of petroleum hydrocarbons through synergistic action. The interaction force between catalytic enzymes and petroleum hydrocarbons was mainly hydrophobic interaction, with some π-π stacking interaction. This study conducted the first molecular simulation of anaerobic degradation of petroleum hydrocarbons, illustrating the interaction mode between petroleum hydrocarbons and enzymes, as well as the anaerobic degradation mechanism of petroleum hydrocarbons.

{"title":"Molecular docking simulation of anaerobic biodegradation pathways of petroleum hydrocarbons in oil reservoir","authors":"Shiqi Wang , Qichao Xie , Haitong Yang , Xiaodong Chen , Wen Liu , Congcong Li , Shuoliang Wang","doi":"10.1016/j.ibiod.2024.105972","DOIUrl":"10.1016/j.ibiod.2024.105972","url":null,"abstract":"<div><div>In-depth study of the anaerobic biodegradation mechanism of petroleum hydrocarbons is of great significance for microbial oil recovery and bioremediation. This study retrieved microorganisms with genes for anaerobic hydrocarbon degradation from the PATRIC and NCBI databases, and compiled taxonomic information of core microorganisms containing multiple functional genes. Molecular docking simulations were conducted on 11 enzymes involved in the initial degradation pathways, such as fumarate addition reaction, anaerobic hydroxylation, and anaerobic carboxylation. The simulations revealed the petroleum hydrocarbon binding energy, binding affinity, and binding site within the enzyme cavity. The results indicated that the core microbial bacterial lineages with anaerobic degradation functional genes mainly included Bacillota and Proteobacteria. Enzymes in the same initial degradation pathway continuously catalysed the anaerobic degradation of petroleum hydrocarbons through synergistic action. The interaction force between catalytic enzymes and petroleum hydrocarbons was mainly hydrophobic interaction, with some π-π stacking interaction. This study conducted the first molecular simulation of anaerobic degradation of petroleum hydrocarbons, illustrating the interaction mode between petroleum hydrocarbons and enzymes, as well as the anaerobic degradation mechanism of petroleum hydrocarbons.</div></div>","PeriodicalId":13643,"journal":{"name":"International Biodeterioration & Biodegradation","volume":"198 ","pages":"Article 105972"},"PeriodicalIF":4.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143164690","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Analysis of benzene, toluene, ethylbenzene, xylene(s) biodegradation under anoxic conditions using response surface methodology

IF 4.1 2区环境科学与生态学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

International Biodeterioration & Biodegradation

Pub Date : 2025-02-01 DOI: 10.1016/j.ibiod.2024.105973

Gurpreet Kaur , Satyam Verma , Magdalena Krol , Satinder Kaur Brar

The biodegradation potential and metabolism of bacteria depend on the terminal electron acceptors present at contaminated sites. Due to the quick consumption of oxygen, microorganisms tend to use substitute electron acceptors such as nitrate, sulfate, manganese, and iron for biodegradation. The present study aims to investigate the effect of electron acceptors (nitrate, sulfate, and ferric ions) on BTEX biodegradation using Bacillus infantis (B. infantis) and Microbacterium esteraromaticum (M. esteraromaticum). The experiment was designed with response surface methodology using the Box-Behnken method. All four compounds of BTEX biodegraded with removal efficiencies ranging from 46% to 57% in Bacillus-treated samples, while 88–98% biodegradation in Microbacterium-treated cultures. The optimal growth of B. infantis was observed at 250 mg/L of nitrate and iron, while no effect of sulfate was observed. For M. esteraromaticum, 250 mg/L of nitrate and sulfate showed the maximum growth of more than 1 optical density (OD), however, no change in growth was noticed with iron treatment. The investigation showed a maximum BTEX biodegradation of 57% by B. infantis under sulfate reduction and overall, 98% by M. esteraromaticum in combined nitrate and sulfate reduction. The present work provides new insights into soil microbial community responses to electron acceptors under anoxic conditions, signifying that intrinsic microorganisms could be successfully stimulated for ISB with electron acceptors as a supplement.

{"title":"Analysis of benzene, toluene, ethylbenzene, xylene(s) biodegradation under anoxic conditions using response surface methodology","authors":"Gurpreet Kaur , Satyam Verma , Magdalena Krol , Satinder Kaur Brar","doi":"10.1016/j.ibiod.2024.105973","DOIUrl":"10.1016/j.ibiod.2024.105973","url":null,"abstract":"<div><div>The biodegradation potential and metabolism of bacteria depend on the terminal electron acceptors present at contaminated sites. Due to the quick consumption of oxygen, microorganisms tend to use substitute electron acceptors such as nitrate, sulfate, manganese, and iron for biodegradation. The present study aims to investigate the effect of electron acceptors (nitrate, sulfate, and ferric ions) on BTEX biodegradation using <em>Bacillus infantis (B. infantis)</em> and <em>Microbacterium esteraromaticum (M. esteraromaticum)</em>. The experiment was designed with response surface methodology using the Box-Behnken method. All four compounds of BTEX biodegraded with removal efficiencies ranging from 46% to 57% in Bacillus-treated samples, while 88–98% biodegradation in Microbacterium-treated cultures. The optimal growth of <em>B. infantis</em> was observed at 250 mg/L of nitrate and iron, while no effect of sulfate was observed. For <em>M. esteraromaticum</em>, 250 mg/L of nitrate and sulfate showed the maximum growth of more than 1 optical density (OD), however, no change in growth was noticed with iron treatment. The investigation showed a maximum BTEX biodegradation of 57% by <em>B. infantis</em> under sulfate reduction and overall, 98% by <em>M. esteraromaticum</em> in combined nitrate and sulfate reduction. The present work provides new insights into soil microbial community responses to electron acceptors under anoxic conditions, signifying that intrinsic microorganisms could be successfully stimulated for ISB with electron acceptors as a supplement.</div></div>","PeriodicalId":13643,"journal":{"name":"International Biodeterioration & Biodegradation","volume":"198 ","pages":"Article 105973"},"PeriodicalIF":4.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143164691","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Niche differentiation of denitrifying anaerobic methane oxidation bacteria and archaea in the permafrost peatlands

IF 4.1 2区环境科学与生态学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

International Biodeterioration & Biodegradation

Pub Date : 2025-02-01 DOI: 10.1016/j.ibiod.2024.105990

Lingyu Fu , Xiangwen Wu , Dalong Ma , Weiping Yin , Anwen Liu , Xu Wang

The anaerobic oxidation of methane (AOM) coupled to either nitrite or nitrate reduction (nitrite or nitrate-DAMO) is a process connecting global nitrogen and carbon cycles. Permafrost peatlands are important natural sources of methane, and climate warming is accelerating permafrost thaw, resulting in changes in water table and vegetation communities that are dramatically reshaping microbial-mediated methane oxidation processes, potentially creating strong positive peatland-climate feedbacks, while the ecology of DAMO bacteria and archaea in peatland soils is poorly understood. Herein, the diversity, abundance, phylogeny, and potential activity of DAMO bacteria and archaea were explored using molecular techniques and stable isotope tracing in three typical peatlands of the Greater Khingan Mountains permafrost regions. The results revealed the co-existence of DAMO bacteria and archaea, with notable variations in community structures across different peatlands, while the vertical distribution within soil profiles remained relatively stable. These variations were mainly affected by factors such as water content, total organic carbon, nitrite, and nitrate in soil. The potential activity and abundance suggested that DAMO bacteria were predominantly found in the middle soil layers, whereas DAMO archaea were more abundant in the bottom layers. Furthermore, the diversity, potential activity, and abundance of DAMO bacteria generally declined along the forest-peatland ecotone, whereas DAMO archaea exhibited an increasing trend. Partial least squares path modeling (PLS-PM) and correlation analyses revealed strong associations between DAMO activities and the abundances of the pmoA and mcrA genes, in addition to substrate availability. The relative contribution of nitrite-DAMO to the total CH₄ oxidation was 16.77%, slightly higher than that of nitrate-DAMO at 13.23%, with both contributing more significantly than AOM coupled to iron oxide reduction (Fe-AOM) at 8.65%, demonstrating that AOM are important processes for mitigating CH₄ emissions in peatlands. This research contributes to a better understanding of the biogeochemical cycling of CH₄ in permafrost peatlands and broaden our insight into the environmental significance of DAMO microorganisms.

{"title":"Niche differentiation of denitrifying anaerobic methane oxidation bacteria and archaea in the permafrost peatlands","authors":"Lingyu Fu , Xiangwen Wu , Dalong Ma , Weiping Yin , Anwen Liu , Xu Wang","doi":"10.1016/j.ibiod.2024.105990","DOIUrl":"10.1016/j.ibiod.2024.105990","url":null,"abstract":"<div><div>The anaerobic oxidation of methane (AOM) coupled to either nitrite or nitrate reduction (nitrite or nitrate-DAMO) is a process connecting global nitrogen and carbon cycles. Permafrost peatlands are important natural sources of methane, and climate warming is accelerating permafrost thaw, resulting in changes in water table and vegetation communities that are dramatically reshaping microbial-mediated methane oxidation processes, potentially creating strong positive peatland-climate feedbacks, while the ecology of DAMO bacteria and archaea in peatland soils is poorly understood. Herein, the diversity, abundance, phylogeny, and potential activity of DAMO bacteria and archaea were explored using molecular techniques and stable isotope tracing in three typical peatlands of the Greater Khingan Mountains permafrost regions. The results revealed the co-existence of DAMO bacteria and archaea, with notable variations in community structures across different peatlands, while the vertical distribution within soil profiles remained relatively stable. These variations were mainly affected by factors such as water content, total organic carbon, nitrite, and nitrate in soil. The potential activity and abundance suggested that DAMO bacteria were predominantly found in the middle soil layers, whereas DAMO archaea were more abundant in the bottom layers. Furthermore, the diversity, potential activity, and abundance of DAMO bacteria generally declined along the forest-peatland ecotone, whereas DAMO archaea exhibited an increasing trend. Partial least squares path modeling (PLS-PM) and correlation analyses revealed strong associations between DAMO activities and the abundances of the <em>pmoA</em> and <em>mcrA</em> genes, in addition to substrate availability. The relative contribution of nitrite-DAMO to the total CH<sub>4</sub> oxidation was 16.77%, slightly higher than that of nitrate-DAMO at 13.23%, with both contributing more significantly than AOM coupled to iron oxide reduction (Fe-AOM) at 8.65%, demonstrating that AOM are important processes for mitigating CH<sub>4</sub> emissions in peatlands. This research contributes to a better understanding of the biogeochemical cycling of CH<sub>4</sub> in permafrost peatlands and broaden our insight into the environmental significance of DAMO microorganisms.</div></div>","PeriodicalId":13643,"journal":{"name":"International Biodeterioration & Biodegradation","volume":"198 ","pages":"Article 105990"},"PeriodicalIF":4.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143164775","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Insights into mechanism of 1-hydroxy-2-naphthoic acid accumulation during phenanthrene degradation by Stutzerimonas frequens SL-6

IF 4.1 2区环境科学与生态学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

International Biodeterioration & Biodegradation

Pub Date : 2025-02-01 DOI: 10.1016/j.ibiod.2024.105975

Liwei Guo , Xinyu Zhang , Qiang Hou , Hailei Wei , Yilin Gu , Baisuo Zhao , Haisheng Wang

Oxygenated polycyclic aromatic hydrocarbons (oxy-PAHs) represent intermediate metabolites accumulating during the degradation of polycyclic aromatic hydrocarbons (PAHs), posing challenges to effective remediation of PAH contamination. Notably, 1-hydroxy-2-naphthoic acid (1H2N), distinguished by its heightened toxicity, emerges as a pivotal model compound for investigating oxy-PAHs. This research endeavors to unravel the mechanism behind the accumulation of 1H2N by Stutzerimonas frequens SL-6, an efficient phenanthrene-degrading bacterium. Genomic analysis of S. frequens SL-6 implicated nahA, salA, and nahR in the accumulation process of 1H2N. This hypothesis was validated through in vitro assessments of enzyme catalytic activity, reinforced by in vivo gene knockout and complementation studies. Our findings pinpoint SalA as a critical factor in the accumulation of 1H2N. Subsequently, the overexpression of SalA in S. frequens SL-6 led to a 70% reduction in the accumulation of 1H2N. These insights deepen the global understanding of microbial PAHs degradation processes and provide a theoretical foundation for the development of microbial strains capable of efficiently and thoroughly degrading PAHs.

{"title":"Insights into mechanism of 1-hydroxy-2-naphthoic acid accumulation during phenanthrene degradation by Stutzerimonas frequens SL-6","authors":"Liwei Guo , Xinyu Zhang , Qiang Hou , Hailei Wei , Yilin Gu , Baisuo Zhao , Haisheng Wang","doi":"10.1016/j.ibiod.2024.105975","DOIUrl":"10.1016/j.ibiod.2024.105975","url":null,"abstract":"<div><div>Oxygenated polycyclic aromatic hydrocarbons (oxy-PAHs) represent intermediate metabolites accumulating during the degradation of polycyclic aromatic hydrocarbons (PAHs), posing challenges to effective remediation of PAH contamination. Notably, 1-hydroxy-2-naphthoic acid (1H2N), distinguished by its heightened toxicity, emerges as a pivotal model compound for investigating oxy-PAHs. This research endeavors to unravel the mechanism behind the accumulation of 1H2N by <em>Stutzerimonas frequens</em> SL-6, an efficient phenanthrene-degrading bacterium. Genomic analysis of <em>S. frequens</em> SL-6 implicated <em>nahA, salA,</em> and <em>nahR</em> in the accumulation process of 1H2N. This hypothesis was validated through <em>in vitro</em> assessments of enzyme catalytic activity, reinforced by <em>in vivo</em> gene knockout and complementation studies. Our findings pinpoint SalA as a critical factor in the accumulation of 1H2N. Subsequently, the overexpression of SalA in <em>S. frequens</em> SL-6 led to a 70% reduction in the accumulation of 1H2N. These insights deepen the global understanding of microbial PAHs degradation processes and provide a theoretical foundation for the development of microbial strains capable of efficiently and thoroughly degrading PAHs.</div></div>","PeriodicalId":13643,"journal":{"name":"International Biodeterioration & Biodegradation","volume":"198 ","pages":"Article 105975"},"PeriodicalIF":4.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143164663","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genome and transcriptome analysis of the lignite-degrading Trichoderma cf. simile WF8 strain highlights potential degradation mechanisms

IF 4.1 2区环境科学与生态学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

International Biodeterioration & Biodegradation

Pub Date : 2025-02-01 DOI: 10.1016/j.ibiod.2025.105997

Jinghua Yao , Yajuan Chen , Deyu Zhuo , Siqiao Chen , Baichao Xu , Congwei Yan , Wanrong Li , Hui Feng , Sheng Deng , Feng M. Cai , Andrei S. Steindorff , Irina S. Druzhinina , Lei Xiao , Lihui Wei , Paul Daly

The biodegradation of lignite (brown coal) by microorganisms has the potential for bioremediation of contaminated mining sites and to generate alternative ways to valorize lignite, such as by producing humic acids or building block chemicals. Previously, a lignite-degrading strain of Trichoderma was isolated, but the genomic and transcriptomic basis of its lignite-degrading ability remained unknown. Here we report that the sequenced genome of the T. cf. simile WF8 strain encoded for enzymes with roles in the degradation of lignite, and potentially tolerance to lignite-breakdown products. There was only a small number of annotated unique genes in the T. cf. simile WF8 genome compared to other fungi, and likely the expression of gene families shared with other fungi is a key factor in lignite biosolubilization by T. cf. simile. The transcriptomes were analyzed of T. cf. simile cultured at two time-points with the lignite-breakdown model compounds 4-phenoxybenzoic acid (which was growth inhibitory), and phenetole and 9-10-dibutoxyanthracene (neither of which inhibited growth), and showed ∼20% of genes up-regulated by one or more of these compounds. The analysis highlights candidates for characterization and engineering enzyme over-expressing T. cf. simile strains with potentially improved degradation capacity, e.g., laccases and peroxidases, or tolerance and catabolism of breakdown products, e.g., cytochrome P450s, and ring cleavage dioxygenases.

{"title":"Genome and transcriptome analysis of the lignite-degrading Trichoderma cf. simile WF8 strain highlights potential degradation mechanisms","authors":"Jinghua Yao , Yajuan Chen , Deyu Zhuo , Siqiao Chen , Baichao Xu , Congwei Yan , Wanrong Li , Hui Feng , Sheng Deng , Feng M. Cai , Andrei S. Steindorff , Irina S. Druzhinina , Lei Xiao , Lihui Wei , Paul Daly","doi":"10.1016/j.ibiod.2025.105997","DOIUrl":"10.1016/j.ibiod.2025.105997","url":null,"abstract":"<div><div>The biodegradation of lignite (brown coal) by microorganisms has the potential for bioremediation of contaminated mining sites and to generate alternative ways to valorize lignite, such as by producing humic acids or building block chemicals. Previously, a lignite-degrading strain of <em>Trichoderma</em> was isolated, but the genomic and transcriptomic basis of its lignite-degrading ability remained unknown. Here we report that the sequenced genome of the <em>T.</em> cf. <em>simile</em> WF8 strain encoded for enzymes with roles in the degradation of lignite, and potentially tolerance to lignite-breakdown products. There was only a small number of annotated unique genes in the <em>T.</em> cf. <em>simile</em> WF8 genome compared to other fungi, and likely the expression of gene families shared with other fungi is a key factor in lignite biosolubilization by <em>T.</em> cf. <em>simile</em>. The transcriptomes were analyzed of <em>T.</em> cf. <em>simile</em> cultured at two time-points with the lignite-breakdown model compounds 4-phenoxybenzoic acid (which was growth inhibitory), and phenetole and 9-10-dibutoxyanthracene (neither of which inhibited growth), and showed ∼20% of genes up-regulated by one or more of these compounds. The analysis highlights candidates for characterization and engineering enzyme over-expressing <em>T.</em> cf. <em>simile</em> strains with potentially improved degradation capacity, <em>e.g</em>., laccases and peroxidases, or tolerance and catabolism of breakdown products, <em>e.g.</em>, cytochrome P450s, and ring cleavage dioxygenases.</div></div>","PeriodicalId":13643,"journal":{"name":"International Biodeterioration & Biodegradation","volume":"198 ","pages":"Article 105997"},"PeriodicalIF":4.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143165453","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Lignite degraded by Trichoderma citrinoviride: Products, processes and mechanisms 黄绿木霉降解褐煤：产物、过程和机理

IF 4.1 2区环境科学与生态学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

International Biodeterioration & Biodegradation

Pub Date : 2024-11-30 DOI: 10.1016/j.ibiod.2024.105957

Xingyu Mu , Meitong Li , Jianhua Tian , Wenjiao Yuan , Hui Shen , Ruijie Zhang , Shuwei Li , Xin Feng , Xuening Fei , Yuhong Xie

The biodegradation of lignite facilitates the efficient utilization of low-rank coal, and its degradation products, processes, and mechanisms are important areas of research. In this study, the biodegradation process of the lignite was analyzed using scanning electron microscopy (SEM), X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR), and gas chromatography-mass spectrometry (GC-MS). Firstly, the structural changes of lignite caused by Trichoderma citrinoviride were analyzed. Secondly, the main product detected by GC-MS from the degradation of lignite by Trichoderma citrinoviride was identified as erucylamide, with a conversion rate of 12.23%. The main product that was volatilized at 280 °C during the degradation of lignite by Trichoderma citrinoviride was first identified by GC-MS. Finally, the oxidase, LiP, MnP, Lac, and PPO secreted by Trichoderma citrinoviride were the main factors contributing to the degradation of lignite, and the degradation processes and mechanisms were inferred based on enzyme activities. This study provides fundamental experiments and data support for research on lignite in the field of the biochemical industry.

褐煤的生物降解为低阶煤的高效利用提供了便利，其降解产物、过程和机理是研究的重要领域。本研究采用扫描电镜（SEM）、x射线衍射（XRD）、傅里叶变换红外光谱（FT-IR）、气相色谱-质谱（GC-MS）分析了褐煤的生物降解过程。首先，分析了黄绿木霉对褐煤结构的影响。其次，黄绿木霉降解褐煤的GC-MS主要检测产物为乙酰氨基乙酰胺，转化率为12.23%。黄绿木霉在280℃降解褐煤过程中挥发的主要产物首次通过气相色谱-质谱法鉴定。最后，黄绿木霉分泌的氧化酶、LiP、MnP、Lac和PPO是褐煤降解的主要因子，并根据酶活性推断了褐煤的降解过程和机制。本研究为褐煤在生化工业领域的研究提供了基础实验和数据支持。

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引用次数: 0

Antifouling activity exhibited by pyrrolo compound isolated from marine sponge associated bacterium Halobacillus kuroshimensis SNSAB01 against barnacles 从海绵伴生菌黑岛盐杆菌SNSAB01中分离的吡咯啉化合物对藤壶的防污活性研究

IF 4.1 2区环境科学与生态学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

International Biodeterioration & Biodegradation

Pub Date : 2024-11-29 DOI: 10.1016/j.ibiod.2024.105960

S. Nalini , S. Venkatnarayanan , D. Inbakandan , Clarita Clements , S.U. Mohammed Riyaz , T. Stalin Dhas , P. Sriyutha Murthy , G. Dharani

The increasing use of natural products from marine organisms and their synthetic analogs as antifouling agents is replacing chemical biocides due to their ecological compatibility. This study evaluated the antifouling potential of pyrrolo compound (PC) from the sponge-associated bacterium Halobacillus kuroshimensis against the barnacle Amphibalanus reticulatus larval survival, metamorphosis and settlement in the laboratory. The successful concentrations were also subjected to field based static immersion tests to study the efficacy of the PC extract on macrofouling settlement. Results showed decreased naupliar survival and affected larval metamorphosis in a dose-dependent manner, with varying sensitivity among developmental stages. Higher PC concentrations significantly reduced cyprid yield and settlement, with over 50% of cyprid larvae failing to settle at concentrations of 1300 μg/ml and above. Field experiments confirmed a steady decline in barnacle settlement on PC-treated coupons, with less than 50% settlement observed at concentrations of 500–2000 μg/ml over 50 days. The LC₅₀/EC₅₀ ratio for nauplius N-II was 1.11, with higher ratios observed in later stages and for the cypris (1.66), suggesting moderate toxicity and a narrow margin of safety. These ratios suggest barnacle settlement inhibition occurring through a toxic mechanism. The results demonstrate the compound's ability to disrupt barnacle settlement, but also raise concerns about its environmental impact (long-term usage), particularly the potential risks to non-target species before using the compound in real-world antifouling applications. Despite higher concentrations used compared to previous reports, PC shows potential as an effective natural antifouling compound.

由于其生态兼容性，越来越多地使用海洋生物的天然产物及其合成类似物作为防污剂，正在取代化学杀菌剂。本研究在实验室研究了海绵体相关菌黑岛盐杆菌（Halobacillus kuroshimensis）的pyrrolo化合物（PC）对网纹Amphibalanus reticulatus幼虫的生存、蜕变和沉降的防污潜力。还对成功的浓度进行了基于现场的静态浸泡试验，以研究PC提取物对宏观污垢沉降的影响。结果显示，剂量依赖性地降低了幼虫的存活率并影响了幼虫的变态，在不同的发育阶段具有不同的敏感性。较高的PC浓度显著降低了塞浦路斯的产量和沉降，在1300 μg/ml及以上的浓度下，超过50%的塞浦路斯幼虫不能沉降。现场实验证实，在pc处理过的样品上，藤壶沉降稳步下降，在500-2000 μg/ml浓度下，50天内的沉降低于50%。naplius N-II的LC50/EC50比值为1.11，后期较高，鲤的LC50/EC50比值为1.66，毒性中等，安全边际较窄。这些比率表明藤壶沉降抑制是通过毒性机制发生的。研究结果表明，该化合物具有破坏藤壶沉降的能力，但也引起了人们对其环境影响（长期使用）的担忧，特别是在将该化合物用于实际防污应用之前，对非目标物种的潜在风险。尽管与之前的报道相比，PC的使用浓度更高，但它显示出作为一种有效的天然防污化合物的潜力。

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引用次数: 0

Biochemical and chemical markers associated with biodeterioration agents isolated from archive audio-visual materials 从档案音像资料中分离出与生物劣化剂有关的生化标记

IF 4.1 2区环境科学与生态学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

International Biodeterioration & Biodegradation

Pub Date : 2024-11-28 DOI: 10.1016/j.ibiod.2024.105959

Tereza Branysova , Michał Komar , Justyna Szulc , Marcin Sypka , Joanna Nizioł , Aneta Płaza-Altamer , Teresa Stryszewska , Konrad Olejnik , Tomasz Ruman , Beata Gutarowska

Biodeterioration of cultural heritage objects, including audio-visual materials, is driven by complex microbial metabolic processes that remain incompletely understood. This research addresses this gap through a model study using bacterial (Bacillus spp.) and fungal (Alternaria, Aspergillus, and Penicillium spp.) isolates on archival photographs with different binders—albumen, collodion, and gelatine. We examined the enzymatic activities, metabolomic profiles, and structural impacts of microbial colonisation over a two-month period. Isolates demonstrated specific degradation capabilities, with proteolytic and cellulolytic activities prominently observed. Metabolomic analysis revealed a significant production of carboxylic acids and organooxygen compounds across all isolates and binders, indicating common biodegradation pathways involving the breakdown of complex molecules such as cellulose. Gelatine emerged as the most conducive substrate for microbial growth and metabolic activity, exhibiting distinct metabolic profiles compared to collodion and albumen. SEM analysis uncovered preferential colonisation patterns, notably the preference of the Alternaria genus for collodion. The microbial activity resulted in measurable changes in pH, colour, and mechanical properties of the materials, with albumen elongation drastically reduced to 0.76%. Our findings elucidate the microbial metabolic processes driving the biodeterioration of photographic materials, providing crucial insights for developing targeted preservation strategies to safeguard audio-visual cultural heritage.

文化遗产（包括音像资料）的生物劣化是由复杂的微生物代谢过程引起的，而人们对这一过程的了解还很不够。本研究通过一项模型研究，利用细菌（芽孢杆菌属）和真菌（交替孢霉属、曲霉属和青霉属）分离物对不同粘合剂（阿尔伯烯、胶版纸和明胶）的档案照片进行研究，填补了这一空白。我们在两个月的时间里研究了微生物定植的酶活性、代谢组学特征和结构影响。分离菌展示了特定的降解能力，其中蛋白质分解和纤维素分解活性最为突出。代谢组学分析表明，所有分离物和粘合剂都会产生大量羧酸和有机氧化合物，这表明生物降解的共同途径涉及分解纤维素等复杂分子。明胶是最有利于微生物生长和新陈代谢活动的基质，与胶棉和蛋白相比，明胶表现出独特的新陈代谢特征。扫描电子显微镜分析发现了优先定殖模式，尤其是交替孢属对胶乳的偏好。微生物活动导致材料的 pH 值、颜色和机械性能发生了可测量的变化，白蛋白的伸长率大幅降低至 0.76%。我们的研究结果阐明了驱动照相材料生物劣化的微生物代谢过程，为制定有针对性的保存策略以保护视听文化遗产提供了重要的启示。

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引用次数: 0

Biodeterioration of chrome-tanned leather and its prevention strategies 铬鞣皮革的生物劣化及其预防策略

IF 4.1 2区环境科学与生态学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

International Biodeterioration & Biodegradation

Pub Date : 2024-11-27 DOI: 10.1016/j.ibiod.2024.105961

Yuxin Song , Zhengyi Sun , Fengxiang Luo , Xu Zhang , Biyu Peng

Preventing biodeterioration of chrome-tanned leather due to mold growth during storage is critical in the leather industry. In this paper, Differential Scanning Calorimeter (DSC), Inductively Coupled Plasma-Atomic Emission Spectroscopy (ICP-AES), Liquid Chromatography-Mass Spectrometry (LC-MS) and characteristic components analysis were used to analyze the biodeterioration process and mechanism of the chrome-tanned leather. Feasible strategies to improve the biodeterioration prevention effect were explored in detail from the aspect of tanning-basification processes and the selection of fungicides. The results showed that molds grow and reproduce by using the available proteins, fats and carbohydrates in the chrome-tanned leather as nutrient resources, metabolizing and secreting alkaline substances such as histamine and spermine, and proteases, simultaneously. The macromolecular organic matter was hydrolyzed into small molecular substances and provided nutrients for microorganisms, meanwhile, the increase of environmental pH caused the dechroming of tanned collagen fiber, accelerating the degradation of collagen fiber, making tanned leather more easily destroyed. Furthermore, the use of a proper amount of MgO for basification was not likely to cause a continuous increase in the pH of the chrome-tanned leather during storage, and the pH of the leather eventually stabilized at about 4.0 during long-term storage. Additionally, the use of 100 mg/L of fungicides MIT, CMIT, IPBC and OIT can effectively kill molds and continuously inhibit the development of mold spores during the storage procedure, which is an effective way to solve biodeterioration of chrome-tanned leather. Hence, this study provides theoretical support for effectively solving the problem of biodegradation of chrome-tanned leather caused by mold growth and reproduction, which could reduce the hazard to the environment while reducing the production cost of tanneries and improving the economic benefits.

防止铬鞣革在贮存期间因霉菌生长而发生生物劣化是皮革行业的关键所在。本文采用差示扫描量热仪（DSC）、电感耦合等离子体原子发射光谱法（ICP-AES）、液相色谱-质谱法（LC-MS）和特征成分分析法对铬鞣革的生物劣化过程和机理进行了分析。从鞣制-碱化工艺和杀菌剂的选择方面详细探讨了提高生物劣化预防效果的可行策略。结果表明，霉菌利用铬鞣皮革中的蛋白质、脂肪和碳水化合物作为营养资源，同时代谢和分泌组胺、精胺等碱性物质和蛋白酶，从而生长和繁殖。大分子有机物被水解成小分子物质，为微生物提供了营养，同时，环境 pH 值的升高导致鞣革胶原纤维脱色，加速了胶原纤维的降解，使鞣革更容易被破坏。此外，使用适量的氧化镁进行碱化也不会导致铬鞣革的 pH 值在储存过程中持续升高，在长期储存过程中，皮革的 pH 值最终稳定在 4.0 左右。此外，使用 100 mg/L 的杀菌剂 MIT、CMIT、IPBC 和 OIT 可以有效杀死霉菌，并在贮藏过程中持续抑制霉菌孢子的发展，是解决铬鞣革生物劣化的有效方法。因此，本研究为有效解决霉菌生长繁殖引起的铬鞣革生物降解问题提供了理论支持，在降低制革厂生产成本、提高经济效益的同时，也可减少对环境的危害。

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引用次数: 0