Pub Date : 2025-09-13DOI: 10.1016/j.ibiod.2025.106211
Yaling Gou , Hongwei Pang , Naijin Wu , Ji Zhang , Xiang Li , Jiajia Wang , Lingze Zeng , Longyi Wei , Rifeng Kang , Wenxia Wei , Peizhong Li
Cocontamination by chlorinated hydrocarbons (CHs) and heavy metals (HMs) frequently occurs at electroplating plant sites. However, how these two types of pollutants interact to influence native microbial communities, and how these communities respond to such combined stress, remains unclear. In this study, the distribution of pollutants and the response characteristics of bacteria and organohalide-respiring bacteria (OHRB) in CH–HM-contaminated soil collected from an electroplating plant of a former auto parts manufacturing company were examined. The two pollutant types exhibited distinct vertical spatial distributions. Soil bacterial communities were affected primarily by depth, followed by soil texture and pollutant concentration. Specifically, trichloroethylene, vinyl chloride, chromium (Cr), zinc, nickel, and Cr6+ levels in the soil were key factors influencing the relative abundance of bacterial phyla. Nevertheless, the abundance of OHRB (Geobacter) was more indicative of CH contamination than of HM presence. Moreover, soil bacterial functions across different depths, textures, and pollutant concentrations showed no significant differences. The bacterial network was divided into 20 modules, with cooperative (positive) interactions outnumbering competitive (negative) interactions. In total, four bacterial genera within Proteobacteria played a key role in this cocontaminated environment. These findings provide a scientific basis for developing bioremediation strategies for sites affected by CHs and HMs.
{"title":"Response characteristics of microbial community in soil cocontaminated with heavy metals and chlorinated hydrocarbons: A field study at a demolished electroplating plant site","authors":"Yaling Gou , Hongwei Pang , Naijin Wu , Ji Zhang , Xiang Li , Jiajia Wang , Lingze Zeng , Longyi Wei , Rifeng Kang , Wenxia Wei , Peizhong Li","doi":"10.1016/j.ibiod.2025.106211","DOIUrl":"10.1016/j.ibiod.2025.106211","url":null,"abstract":"<div><div>Cocontamination by chlorinated hydrocarbons (CHs) and heavy metals (HMs) frequently occurs at electroplating plant sites. However, how these two types of pollutants interact to influence native microbial communities, and how these communities respond to such combined stress, remains unclear. In this study, the distribution of pollutants and the response characteristics of bacteria and organohalide-respiring bacteria (OHRB) in CH–HM-contaminated soil collected from an electroplating plant of a former auto parts manufacturing company were examined. The two pollutant types exhibited distinct vertical spatial distributions. Soil bacterial communities were affected primarily by depth, followed by soil texture and pollutant concentration. Specifically, trichloroethylene, vinyl chloride, chromium (Cr), zinc, nickel, and Cr<sup>6+</sup> levels in the soil were key factors influencing the relative abundance of bacterial phyla. Nevertheless, the abundance of OHRB (<em>Geobacter</em>) was more indicative of CH contamination than of HM presence. Moreover, soil bacterial functions across different depths, textures, and pollutant concentrations showed no significant differences. The bacterial network was divided into 20 modules, with cooperative (positive) interactions outnumbering competitive (negative) interactions. In total, four bacterial genera within Proteobacteria played a key role in this cocontaminated environment. These findings provide a scientific basis for developing bioremediation strategies for sites affected by CHs and HMs.</div></div>","PeriodicalId":13643,"journal":{"name":"International Biodeterioration & Biodegradation","volume":"206 ","pages":"Article 106211"},"PeriodicalIF":4.1,"publicationDate":"2025-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145045460","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}
Pub Date : 2025-09-13DOI: 10.1016/j.ibiod.2025.106212
Nazish Muzaffar , Shujie Zhang , Qian Li , Yuhui Yang , Yanli Xie , Yuan Tian
Aflatoxin B1 (AFB1) and Zearalenone (ZEN) are highly toxic mycotoxins commonly present in cereal-based foods, making their degradation a crucial research area for ensuring food safety. This study demonstrated that extracellular components mediated the biodegradation of AFB1 and ZEN from Bacillus amyloliquefaciens HNGD-T8, isolated from fermented tea. The cell-free supernatants achieved 99.57 % and 99.9 % degradation at 80 °C for AFB1 and ZEN, respectively. Notably, Mn2+ enhanced the degradation of both mycotoxins. Simultaneous degradation of AFB1 and ZEN was achieved at 78.02 % and 93.74 %, respectively. Ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS/MS) analysis revealed that both mycotoxins were broken down into different metabolites, with AFB1 converting into (C17H12O7, C13H10O4) and ZEN transforming into (C18H22O7, C17H24O4). Degradation of AFB1 and ZEN led to the disruption of their active sites and the formation of derivative compounds. Subsequent toxicity assessment using zebrafish larvae demonstrated that these degradation products exhibited reduced toxicity. In maize flour, AFB1 and ZEN degraded 74.20 % and 59.57 %, respectively, while simultaneous degradation achieved 66.23 % and 78.07 %. Given its potent degradation ability, Mn2+-enhanced activity, thermostability, and effectiveness in maize flour, these findings underscore the promising potential of HNGD-T8 for mitigating mycotoxin contamination in food matrices and contributing to sustainable food safety solutions.
{"title":"Thermostable extracellular enzyme-mediated biodegradation of Aflatoxin B1 and Zearalenone in maize flour: A promising strategy","authors":"Nazish Muzaffar , Shujie Zhang , Qian Li , Yuhui Yang , Yanli Xie , Yuan Tian","doi":"10.1016/j.ibiod.2025.106212","DOIUrl":"10.1016/j.ibiod.2025.106212","url":null,"abstract":"<div><div>Aflatoxin B<sub>1</sub> (AFB<sub>1</sub>) and Zearalenone (ZEN) are highly toxic mycotoxins commonly present in cereal-based foods, making their degradation a crucial research area for ensuring food safety. This study demonstrated that extracellular components mediated the biodegradation of AFB<sub>1</sub> and ZEN from <em>Bacillus amyloliquefaciens</em> HNGD-T8, isolated from fermented tea. The cell-free supernatants achieved 99.57 % and 99.9 % degradation at 80 °C for AFB<sub>1</sub> and ZEN, respectively. Notably, Mn<sup>2+</sup> enhanced the degradation of both mycotoxins. Simultaneous degradation of AFB<sub>1</sub> and ZEN was achieved at 78.02 % and 93.74 %, respectively. Ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS/MS) analysis revealed that both mycotoxins were broken down into different metabolites, with AFB<sub>1</sub> converting into (C<sub>17</sub>H<sub>12</sub>O<sub>7</sub>, C<sub>13</sub>H<sub>10</sub>O<sub>4</sub>) and ZEN transforming into (C<sub>18</sub>H<sub>22</sub>O<sub>7</sub>, C<sub>17</sub>H<sub>24</sub>O<sub>4</sub>). Degradation of AFB<sub>1</sub> and ZEN led to the disruption of their active sites and the formation of derivative compounds. Subsequent toxicity assessment using zebrafish larvae demonstrated that these degradation products exhibited reduced toxicity. In maize flour, AFB<sub>1</sub> and ZEN degraded 74.20 % and 59.57 %, respectively, while simultaneous degradation achieved 66.23 % and 78.07 %. Given its potent degradation ability, Mn<sup>2+</sup>-enhanced activity, thermostability, and effectiveness in maize flour, these findings underscore the promising potential of HNGD-T8 for mitigating mycotoxin contamination in food matrices and contributing to sustainable food safety solutions.</div></div>","PeriodicalId":13643,"journal":{"name":"International Biodeterioration & Biodegradation","volume":"206 ","pages":"Article 106212"},"PeriodicalIF":4.1,"publicationDate":"2025-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145045405","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}
Pub Date : 2025-09-11DOI: 10.1016/j.ibiod.2025.106208
Yunsi Duan , Hongling Zhang , Guofeng Ma
Due to the ongoing emission of organic pollutants, there is an urgent need to find green and sustainable remediation technologies that also offer economic benefits. Rhizoremediation technology, which achieves pollutant degradation through plant-microbe interactions, has emerged as a highly promising green solution. However, complex soil environments and multiple limiting factors restrict its large-scale application. This review systematically discusses plant-microbial interactions, including allelopathy, co-metabolic degradation, defensive interactions, and microbial recruitment. It focuses on analyzing the rhizosphere microbial degradation mechanisms of four common types of organic pollutants: pesticides, polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), and pharmaceuticals and personal care products (PPCPs). For the limiting factors of remediation efficiency, seven enhancement measures are detailed: manure/composting, biochar, surfactants, biofortification, nanomaterials, microbial electrochemical, and genetic modification. Finally, the key challenges and future development directions of each technology in practical applications are explored. This review provides theoretical basis and technical references for the optimization and engineering of rhizosphere remediation technologies.
{"title":"Rhizoremediation of organically contaminated soils: mechanisms, influencing factors and enhancing measures","authors":"Yunsi Duan , Hongling Zhang , Guofeng Ma","doi":"10.1016/j.ibiod.2025.106208","DOIUrl":"10.1016/j.ibiod.2025.106208","url":null,"abstract":"<div><div>Due to the ongoing emission of organic pollutants, there is an urgent need to find green and sustainable remediation technologies that also offer economic benefits. Rhizoremediation technology, which achieves pollutant degradation through plant-microbe interactions, has emerged as a highly promising green solution. However, complex soil environments and multiple limiting factors restrict its large-scale application. This review systematically discusses plant-microbial interactions, including allelopathy, co-metabolic degradation, defensive interactions, and microbial recruitment. It focuses on analyzing the rhizosphere microbial degradation mechanisms of four common types of organic pollutants: pesticides, polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), and pharmaceuticals and personal care products (PPCPs). For the limiting factors of remediation efficiency, seven enhancement measures are detailed: manure/composting, biochar, surfactants, biofortification, nanomaterials, microbial electrochemical, and genetic modification. Finally, the key challenges and future development directions of each technology in practical applications are explored. This review provides theoretical basis and technical references for the optimization and engineering of rhizosphere remediation technologies.</div></div>","PeriodicalId":13643,"journal":{"name":"International Biodeterioration & Biodegradation","volume":"206 ","pages":"Article 106208"},"PeriodicalIF":4.1,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145045459","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}
Pub Date : 2025-09-09DOI: 10.1016/j.ibiod.2025.106210
Sri Auliyah Azis , Dahlang Tahir , Rachid Masrour , Vicram Setiawan , Heryanto Heryanto , Ahmed Akouibaa , Ali Hamed Alomari , Siswanto Siswanto
The increasing demand for nickel in the industrial sector has led to significant Ni2+ contamination in the aquatic environment, especially from mine wastewater. This study successfully synthesized eco-friendly biocomposite adsorbents through a blending-thermal method by integrating activated carbon (AC) from ripe (sample 1) and unripe (sample 2) banana peels with Ca(OH)2 from limestone. The adsorption performance of both biocomposites was evaluated for Ni2+ removal from aqueous solutions. The results indicated that the sample 1/Ca(OH)2 biocomposite attained a removal efficiency of 93 %, marginally surpassing the 92.5 % demonstrated by sample 2/Ca(OH)2, thereby affirming the enhanced adsorption capacity of AC derived from ripe banana peels. Morphological analysis using SEM revealed distinct surface characteristics; with sample 1 resembling oyster mushroom-like structures and sample 2 exhibiting lettuce-like forms, both possessing marshmallow-like surface textures. IoT-based real-time monitoring showed optimal conditions for Ni2+ adsorption at 28–30 °C and low pH. The most significant reduction in absorbance occurred within 200 min due to rapid contact, followed by gradual degradation of pollutants and stabilisation of pH over time. Additionally, the adsorption ability was also attributed to the results of XRD analysis, which showed a decrease in amorphous index with a corresponding increase in crystallinity index upon incorporation of Ca(OH)2, while FTIR spectra confirmed the increased presence of carbonate groups (CO32−), which contributed to the enhanced binding of metal ions.
{"title":"Nickel ion removal from mine wastewater using eco-friendly activated carbon/Ca(OH)2 from banana Peels: IoT-Based real-time monitoring implemented","authors":"Sri Auliyah Azis , Dahlang Tahir , Rachid Masrour , Vicram Setiawan , Heryanto Heryanto , Ahmed Akouibaa , Ali Hamed Alomari , Siswanto Siswanto","doi":"10.1016/j.ibiod.2025.106210","DOIUrl":"10.1016/j.ibiod.2025.106210","url":null,"abstract":"<div><div>The increasing demand for nickel in the industrial sector has led to significant Ni<sup>2+</sup> contamination in the aquatic environment, especially from mine wastewater. This study successfully synthesized eco-friendly biocomposite adsorbents through a blending-thermal method by integrating activated carbon (AC) from ripe (sample 1) and unripe (sample 2) banana peels with Ca(OH)<sub>2</sub> from limestone. The adsorption performance of both biocomposites was evaluated for Ni<sup>2+</sup> removal from aqueous solutions. The results indicated that the sample 1/Ca(OH)<sub>2</sub> biocomposite attained a removal efficiency of 93 %, marginally surpassing the 92.5 % demonstrated by sample 2/Ca(OH)<sub>2</sub>, thereby affirming the enhanced adsorption capacity of AC derived from ripe banana peels. Morphological analysis using SEM revealed distinct surface characteristics; with sample 1 resembling oyster mushroom-like structures and sample 2 exhibiting lettuce-like forms, both possessing marshmallow-like surface textures. IoT-based real-time monitoring showed optimal conditions for Ni<sup>2+</sup> adsorption at 28–30 °C and low pH. The most significant reduction in absorbance occurred within 200 min due to rapid contact, followed by gradual degradation of pollutants and stabilisation of pH over time. Additionally, the adsorption ability was also attributed to the results of XRD analysis, which showed a decrease in amorphous index with a corresponding increase in crystallinity index upon incorporation of Ca(OH)<sub>2</sub>, while FTIR spectra confirmed the increased presence of carbonate groups (CO<sub>3</sub><sup>2−</sup>), which contributed to the enhanced binding of metal ions.</div></div>","PeriodicalId":13643,"journal":{"name":"International Biodeterioration & Biodegradation","volume":"206 ","pages":"Article 106210"},"PeriodicalIF":4.1,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145019378","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}
Pub Date : 2025-09-06DOI: 10.1016/j.ibiod.2025.106204
Ji-Dong Gu
Scientific research can be conducted at several levels, conceptual, mechanistic or observation description. It is evident that an increasing number of manuscripts are using optimization of an engineering process or system to generate results for the contents of an intended manuscript. This phenomenon is especially prevalent in research in applied engineering and applied science when innovative research hypothesis is apparently lacking. The weakness of doing in this way is that a high impact scientific question is not identified and focused for an important research topic leading to a publication. The optimization parameters may be useful for practical application and implementation. It shall be clearly distinguished between these two, so that an effective research planning can be made to advance science for knowledge and engineering for practical application to improve living quality.
{"title":"Does optimization contribute to fundamental science significantly?","authors":"Ji-Dong Gu","doi":"10.1016/j.ibiod.2025.106204","DOIUrl":"10.1016/j.ibiod.2025.106204","url":null,"abstract":"<div><div>Scientific research can be conducted at several levels, conceptual, mechanistic or observation description. It is evident that an increasing number of manuscripts are using optimization of an engineering process or system to generate results for the contents of an intended manuscript. This phenomenon is especially prevalent in research in applied engineering and applied science when innovative research hypothesis is apparently lacking. The weakness of doing in this way is that a high impact scientific question is not identified and focused for an important research topic leading to a publication. The optimization parameters may be useful for practical application and implementation. It shall be clearly distinguished between these two, so that an effective research planning can be made to advance science for knowledge and engineering for practical application to improve living quality.</div></div>","PeriodicalId":13643,"journal":{"name":"International Biodeterioration & Biodegradation","volume":"206 ","pages":"Article 106204"},"PeriodicalIF":4.1,"publicationDate":"2025-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145463017","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}
Pub Date : 2025-09-05DOI: 10.1016/j.ibiod.2025.106205
Sujata Dey , Ajaya Kumar Rout , Koushik Ghosh , Ajoy Saha , Vikash Kumar , Basanta Kumar Das , Bijay Kumar Behera
Polyethylene (PE) constitutes nearly 50% of the total microplastic (MP) waste worldwide, and their accumulation in the environment poses significant ecological concerns. PE persists in the environment for centuries, accumulating in landfills and aquatic ecosystems, where it adsorbs heavy metals and organic pollutants, entering food chains and posing severe ecological and health risks, including endocrine disruption and cellular toxicity. Bioremediation methods using microorganisms to degrade synthetic polymers has emerged as a sustainable alternative. However, only a limited number of microbes have been identified so far, primarily due to the challenges of culturing potential degraders under laboratory conditions and the highly resistant structure of PE. In this study, we isolated two strains, Proteus penneri ND-SD-4709 and Proteus vulgaris BKB-SD-13892, from urban plastic waste disposal sites and investigated their PE-degrading potential. Both strains utilized PE as a carbon source, as confirmed by weight loss (19.13±0.40% for P. penneri ND-SD-4709 and 17.30±0.55% for P. vulgaris BKB-SD-13892), polymer reduction rate (K=0.00177 day−1±0.00003 for P. penneri ND-SD-4709 and 0.00158 day−1±0.00006 for P. vulgaris BKB-SD-13892), and calculation of half-life (t1/2=391.80±8.69 for P. penneri ND-SD-4709 and 438.22±15.31 for P. vulgaris BKB-SD-13892) after 120 days of incubation in a carbon-free medium. Biodegradation was further validated using fourier transform infrared spectroscopy (FT-IR), which showed structural alterations, and field emission scanning electron microscopy (FE-SEM), which revealed surface erosion in PE following microbial treatment. Additionally, gas chromatography-mass spectrometry (GC-MS) identified degradation intermediates whose kinetic profiling revealed superior polyethylene degradation efficacy through biodegradation efficiency metrics. The results demonstrate that P. penneri ND-SD-4709 exhibits faster and more consistent polyethylene degradation kinetics than P. vulgaris BKB-SD-13892. Our work offers a laboratory-based comparative analysis of two different underexplored Proteus spp., followed by effective methodological framework for isolation, selection, and evaluation of specific polymer-degrading microorganisms using advanced analytical techniques. These findings have significant implications for developing PE-waste management strategies like enzyme characterization, metabolic engineering, and field-scale validation to enhance degradation kinetics.
{"title":"Proteus spp. as potential agents for polyethylene (PE) bioremediation: Isolation, identification, and comparative degradation analysis","authors":"Sujata Dey , Ajaya Kumar Rout , Koushik Ghosh , Ajoy Saha , Vikash Kumar , Basanta Kumar Das , Bijay Kumar Behera","doi":"10.1016/j.ibiod.2025.106205","DOIUrl":"10.1016/j.ibiod.2025.106205","url":null,"abstract":"<div><div>Polyethylene (PE) constitutes nearly 50% of the total microplastic (MP) waste worldwide, and their accumulation in the environment poses significant ecological concerns. PE persists in the environment for centuries, accumulating in landfills and aquatic ecosystems, where it adsorbs heavy metals and organic pollutants, entering food chains and posing severe ecological and health risks, including endocrine disruption and cellular toxicity. Bioremediation methods using microorganisms to degrade synthetic polymers has emerged as a sustainable alternative. However, only a limited number of microbes have been identified so far, primarily due to the challenges of culturing potential degraders under laboratory conditions and the highly resistant structure of PE. In this study, we isolated two strains, <em>Proteus penneri</em> ND-SD-4709 and <em>Proteus vulgaris</em> BKB-SD-13892, from urban plastic waste disposal sites and investigated their PE-degrading potential. Both strains utilized PE as a carbon source, as confirmed by weight loss (19.13±0.40% for <em>P. penneri</em> ND-SD-4709 and 17.30±0.55% for <em>P. vulgaris</em> BKB-SD-13892), polymer reduction rate (K=0.00177 day<sup>−1</sup>±0.00003 for <em>P. penneri</em> ND-SD-4709 and 0.00158 day<sup>−1</sup>±0.00006 for <em>P. vulgaris</em> BKB-SD-13892), and calculation of half-life (t<sub>1/2</sub>=391.80±8.69 for <em>P. penneri</em> ND-SD-4709 and 438.22±15.31 for <em>P. vulgaris</em> BKB-SD-13892) after 120 days of incubation in a carbon-free medium. Biodegradation was further validated using fourier transform infrared spectroscopy (FT-IR), which showed structural alterations, and field emission scanning electron microscopy (FE-SEM), which revealed surface erosion in PE following microbial treatment. Additionally, gas chromatography-mass spectrometry (GC-MS) identified degradation intermediates whose kinetic profiling revealed superior polyethylene degradation efficacy through biodegradation efficiency metrics. The results demonstrate that <em>P. penneri</em> ND-SD-4709 exhibits faster and more consistent polyethylene degradation kinetics than <em>P. vulgaris</em> BKB-SD-13892. Our work offers a laboratory-based comparative analysis of two different underexplored <em>Proteus</em> spp., followed by effective methodological framework for isolation, selection, and evaluation of specific polymer-degrading microorganisms using advanced analytical techniques. These findings have significant implications for developing PE-waste management strategies like enzyme characterization, metabolic engineering, and field-scale validation to enhance degradation kinetics.</div></div>","PeriodicalId":13643,"journal":{"name":"International Biodeterioration & Biodegradation","volume":"206 ","pages":"Article 106205"},"PeriodicalIF":4.1,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145004668","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}
Pub Date : 2025-09-04DOI: 10.1016/j.ibiod.2025.106206
Lateef B. Salam , Oluwafemi S. Obayori
Lindane (γ-hexachlorocyclohexane; γ-HCH) is a persistent organochlorine pesticide widely detected in aquatic sediments across low- and middle-income countries, posing significant ecological and public health risks. This study employed high-throughput shotgun metagenomics to profile microbial communities and elucidate the functional gene repertoire underlying the potential for in situ lindane degradation in Afelele pond sediment (APS), a tropical lentic waterbody in Nigeria. Sediment analysis revealed a lindane concentration of 8.23 μg g−1 (dry weight), underscoring its environmental persistence. Metagenomic annotation identified all eleven canonical lindane-degradation genes (linA–linJ), with high-confidence sequence homology across diverse bacterial phyla and limited archaeal and fungal lineage representation. Notably, Betaproteobacteria genera such as Rhodoferax, Polaromonas, Malikia, Limnohabitans, and Sphaerotilus encoded ≥8 lin genes, suggesting potential roles as keystone degraders. Gene-specific taxonomic breadth was highest for linB, linC/X, linI, and linJ, indicating widespread functional redundancy. In contrast, linA, initiating dechlorination, showed restricted taxonomic dispersion, implying a potential bottleneck in natural degradation pathways. The presence of lin genes in previously unreported taxa points to dynamic microbial adaptation and possible horizontal gene transfer. This study provides the first comprehensive metagenomic evidence of complete genetic potential for lindane biodegradation in an African freshwater sediment ecosystem. The findings highlight the robust intrinsic bioremediation potential of indigenous microbial consortia and support the feasibility of in situ bioaugmentation strategies tailored to tropical environments. Future work would focus on validating gene expression and enzyme activity to assess degradation efficacy and inform sustainable biotechnological interventions for persistent organic pollutants.
{"title":"Shotgun metagenomics reveals the complete genetic potential for lindane biodegradation in a tropical lentic pond sediment","authors":"Lateef B. Salam , Oluwafemi S. Obayori","doi":"10.1016/j.ibiod.2025.106206","DOIUrl":"10.1016/j.ibiod.2025.106206","url":null,"abstract":"<div><div>Lindane (γ-hexachlorocyclohexane; γ-HCH) is a persistent organochlorine pesticide widely detected in aquatic sediments across low- and middle-income countries, posing significant ecological and public health risks. This study employed high-throughput shotgun metagenomics to profile microbial communities and elucidate the functional gene repertoire underlying the potential for in situ lindane degradation in Afelele pond sediment (APS), a tropical lentic waterbody in Nigeria. Sediment analysis revealed a lindane concentration of 8.23 μg g<sup>−1</sup> (dry weight), underscoring its environmental persistence. Metagenomic annotation identified all eleven canonical lindane-degradation genes (<em>linA–linJ</em>), with high-confidence sequence homology across diverse bacterial phyla and limited archaeal and fungal lineage representation. Notably, Betaproteobacteria genera such as <em>Rhodoferax</em>, <em>Polaromonas</em>, <em>Malikia</em>, <em>Limnohabitans</em>, and <em>Sphaerotilus</em> encoded ≥8 <em>lin</em> genes, suggesting potential roles as keystone degraders. Gene-specific taxonomic breadth was highest for <em>linB, linC/X, linI,</em> and <em>linJ</em>, indicating widespread functional redundancy. In contrast, <em>linA</em>, initiating dechlorination, showed restricted taxonomic dispersion, implying a potential bottleneck in natural degradation pathways. The presence of <em>lin</em> genes in previously unreported taxa points to dynamic microbial adaptation and possible horizontal gene transfer. This study provides the first comprehensive metagenomic evidence of complete genetic potential for lindane biodegradation in an African freshwater sediment ecosystem. The findings highlight the robust intrinsic bioremediation potential of indigenous microbial consortia and support the feasibility of in situ bioaugmentation strategies tailored to tropical environments. Future work would focus on validating gene expression and enzyme activity to assess degradation efficacy and inform sustainable biotechnological interventions for persistent organic pollutants.</div></div>","PeriodicalId":13643,"journal":{"name":"International Biodeterioration & Biodegradation","volume":"206 ","pages":"Article 106206"},"PeriodicalIF":4.1,"publicationDate":"2025-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144996841","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}
Nitrification is a pivotal nitrogen transformation process in agricultural ecosystems, playing a crucial role in maintaining soil nitrogen balance and ensuring food security. The conversion of ammonia to nitrite—a rate-limiting step in nitrification—is catalyzed by ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and complete ammonia oxidizers (comammox Nitrospira). However, the specific characteristics of ammonia oxidation across different agricultural soils remain poorly understood. In this study, we investigated the community composition and metabolic activity of ammonia oxidizers in four agricultural soils, including green vegetable land (GVL), wasteland farmland (WF), orange planting land (OPL) and sesame planting land (SPL). The results indicate that AOA exhibit a higher abundance compared to AOB and comammox Nitrospira, with groups Ⅰ.1a and Ⅰ.1b identified as the dominant group. Salinity, NH3 and pH were found to significantly influence the community structure of AOA. Neutral model analysis showed that the community assembly of ammonia oxidizers was a stochasticity process (drift) in agricultural soils. Co-occurrence network in GVL and OPL exhibited higher network density and average degree compared to those in WF and SPL. However, a higher proportion of negative correlations was observed in WF and SPL. Stable isotope probing (DNA-SIP) analysis confirmed that 13C was predominantly assimilated by AOA-Ⅰ.1b, with minimal incorporation by AOB-Nitrosomonas and -Nitrosospira. This study provides comprehensive insights into the spatial distribution and activity of ammonia oxidizers in the agricultural soils of the Yangtze River estuary, contributing to a deeper understanding of nitrogen cycling in these ecosystems.
{"title":"Ammonia-oxidizing archaea as dominant and active ammonia oxidizers in agricultural soils from Yangtze River estuary by DNA-SIP","authors":"Xiufeng Tang , Lingyu Guo , Shijie Hua , Xiangyang Zhao , Tianjiao Zhang , Xingpan Guo , Ping Han , Chao Xue , Jun Yuan","doi":"10.1016/j.ibiod.2025.106203","DOIUrl":"10.1016/j.ibiod.2025.106203","url":null,"abstract":"<div><div>Nitrification is a pivotal nitrogen transformation process in agricultural ecosystems, playing a crucial role in maintaining soil nitrogen balance and ensuring food security. The conversion of ammonia to nitrite—a rate-limiting step in nitrification—is catalyzed by ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and complete ammonia oxidizers (comammox <em>Nitrospira</em>). However, the specific characteristics of ammonia oxidation across different agricultural soils remain poorly understood. In this study, we investigated the community composition and metabolic activity of ammonia oxidizers in four agricultural soils, including green vegetable land (GVL), wasteland farmland (WF), orange planting land (OPL) and sesame planting land (SPL). The results indicate that AOA exhibit a higher abundance compared to AOB and comammox <em>Nitrospira</em>, with groups Ⅰ.1a and Ⅰ.1b identified as the dominant group. Salinity, NH<sub>3</sub> and pH were found to significantly influence the community structure of AOA. Neutral model analysis showed that the community assembly of ammonia oxidizers was a stochasticity process (drift) in agricultural soils. Co-occurrence network in GVL and OPL exhibited higher network density and average degree compared to those in WF and SPL. However, a higher proportion of negative correlations was observed in WF and SPL. Stable isotope probing (DNA-SIP) analysis confirmed that <sup>13</sup>C was predominantly assimilated by AOA-Ⅰ.1b, with minimal incorporation by AOB-<em>Nitrosomonas</em> and -<em>Nitrosospira</em>. This study provides comprehensive insights into the spatial distribution and activity of ammonia oxidizers in the agricultural soils of the Yangtze River estuary, contributing to a deeper understanding of nitrogen cycling in these ecosystems.</div></div>","PeriodicalId":13643,"journal":{"name":"International Biodeterioration & Biodegradation","volume":"206 ","pages":"Article 106203"},"PeriodicalIF":4.1,"publicationDate":"2025-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144931652","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}
Pub Date : 2025-09-01DOI: 10.1016/j.ibiod.2025.106170
Ji-Dong Gu
Current research topics on a global scale tend to be more centralized and restricted to some selective ones and the results show a serious lack of research innovation and new discovery. Focusing on transformation and degradation of dyes in environmental science and engineering, I would like to discuss the common features of these manuscripts, some published and others not. The key scientific significant elements of this research topic are also presented, from the catalyst to the process of degradation and further to the stoichiometry of organic carbon balance. The future of science is being affected by the current mass production of similar papers, and the low quality of both the papers and also the researchers are worrisome. It is important to recognize that training in higher education is facing a critically important challenge now and several important courses including philosophy of science, history of science, and scientific methods, should be part of the current curriculum to improve the training.
{"title":"Anything new and significant from recent research on degradation of synthetic dyes?","authors":"Ji-Dong Gu","doi":"10.1016/j.ibiod.2025.106170","DOIUrl":"10.1016/j.ibiod.2025.106170","url":null,"abstract":"<div><div>Current research topics on a global scale tend to be more centralized and restricted to some selective ones and the results show a serious lack of research innovation and new discovery. Focusing on transformation and degradation of dyes in environmental science and engineering, I would like to discuss the common features of these manuscripts, some published and others not. The key scientific significant elements of this research topic are also presented, from the catalyst to the process of degradation and further to the stoichiometry of organic carbon balance. The future of science is being affected by the current mass production of similar papers, and the low quality of both the papers and also the researchers are worrisome. It is important to recognize that training in higher education is facing a critically important challenge now and several important courses including philosophy of science, history of science, and scientific methods, should be part of the current curriculum to improve the training.</div></div>","PeriodicalId":13643,"journal":{"name":"International Biodeterioration & Biodegradation","volume":"205 ","pages":"Article 106170"},"PeriodicalIF":4.1,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144925807","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}
The 2nd International Symposium on Biodeterioration and Protection of Cultural Heritage (Dunhuang, P.R. China, 2024), organized jointly by Dunhuang Academy, Lanzhou University, Guangdong Technion-Israel Institute of Technology, and International Biodeterioration and Biodegradation Society, was held successfully at the renowned Mogao Grottoes on June 20–23, 2024, in Dunhuang of China. This symposium was with an aim to boost and bolster the scientific development and technical progress on biodeterioration and protection in Cultural Heritage conservation, and also promote scientific collaborations among different interested groups crossing boundary of countries and subject areas. It attracted more than 100 experts and scholars from 6 countries, 26 universities and institutes, and 16 cultural and museological units attended this symposium. New cutting-edge achievements and technologies in the field of Cultural Heritage biodeterioration and conservation were shared by the participants during the regular sessions and social hours. The conference themes include microbiome, mechanisms of biodeterioration, new methods and applications for monitoring and biodeterioration research, and bioprotection techniques emerged for restoration and conservation of cultural relics. Cultural Heritage materials of both inorganic and organic in nature were also presented. In addition, challenges and problems raised, and future research trends of this field were proposed and discussed on the symposium.
{"title":"Recent progress on biodeterioration and protection of Cultural Heritage: a conference report of the 2nd international symposium held in Dunhuang, China","authors":"Yuxin Chen , Ji-Dong Gu , Huyuan Feng , Clara Enza Urzì , Fasi Wu","doi":"10.1016/j.ibiod.2025.106132","DOIUrl":"10.1016/j.ibiod.2025.106132","url":null,"abstract":"<div><div>The 2<sup>nd</sup> International Symposium on Biodeterioration and Protection of Cultural Heritage (Dunhuang, P.R. China, 2024), organized jointly by Dunhuang Academy, Lanzhou University, Guangdong Technion-Israel Institute of Technology, and International Biodeterioration and Biodegradation Society, was held successfully at the renowned Mogao Grottoes on June 20–23, 2024, in Dunhuang of China. This symposium was with an aim to boost and bolster the scientific development and technical progress on biodeterioration and protection in Cultural Heritage conservation, and also promote scientific collaborations among different interested groups crossing boundary of countries and subject areas. It attracted more than 100 experts and scholars from 6 countries, 26 universities and institutes, and 16 cultural and museological units attended this symposium. New cutting-edge achievements and technologies in the field of Cultural Heritage biodeterioration and conservation were shared by the participants during the regular sessions and social hours. The conference themes include microbiome, mechanisms of biodeterioration, new methods and applications for monitoring and biodeterioration research, and bioprotection techniques emerged for restoration and conservation of cultural relics. Cultural Heritage materials of both inorganic and organic in nature were also presented. In addition, challenges and problems raised, and future research trends of this field were proposed and discussed on the symposium.</div></div>","PeriodicalId":13643,"journal":{"name":"International Biodeterioration & Biodegradation","volume":"205 ","pages":"Article 106132"},"PeriodicalIF":4.1,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144925806","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}
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