Sulfate-laden acidic wastewater generated from industries and mining activities is a global concern due to its adverse effects. To address this challenge, a bench-scale sulfidogenic semi-batch reactor (SmBR) inoculated with mixed bacterial culture was operated for 281 days to evaluate the effect of sulfate (500–4500 mg/L) and acidic conditions (pH 6.0-1.85) on sulfate removal and microbial communities. The optimum ratio and HRT were found to be 0.7 and 4 days, respectively. The SmBR achieved a sulfate and COD removal of 80 % and 87 %, respectively, with an influent sulfate concentration of 4500 mg/L and a ratio of 0.7, and the effluent pH increased from 2.0 to 7.2. Further decreasing the feed pH to 1.85 resulted in a sharp decline in the reactor performance, which was recovered within 30 days by adjusting operational conditions. Electron flow from lactate to sulfate reduction varied between 86 % and 91 %, demonstrating the effective utilization of substrate. 16S rRNA sequencing revealed that the decrease in influent pH from 6.0 to 2.5 led to a shift in microbial diversity towards a specialized group of SRB, particularly Desulfobacterota (Desulfovibrio genus), which increased from 12 to 45 %, emphasizing their crucial role in sulfate removal. The mixed bacterial culture developed in the SmBR could be suitable for treating industrial sulfate-laden acidic wastewaters such as acid mine drainage, lead acid battery manufacturing wastewater, and secondary lead smelting plant wastewater. The findings of this study offer a sustainable bioremediation approach for treating sulfate-laden acidic wastewater.
{"title":"Biological treatment of sulfate-laden acidic wastewater in a semi-batch reactor: Performance optimization and microbial community dynamics","authors":"Sreekanth Yadav Golla , Guntakala Venkatanaga Chandra , Pranab Kumar Ghosh","doi":"10.1016/j.ibiod.2026.106276","DOIUrl":"10.1016/j.ibiod.2026.106276","url":null,"abstract":"<div><div>Sulfate-laden acidic wastewater generated from industries and mining activities is a global concern due to its adverse effects. To address this challenge, a bench-scale sulfidogenic semi-batch reactor (SmBR) inoculated with mixed bacterial culture was operated for 281 days to evaluate the effect of sulfate (500–4500 mg/L) and acidic conditions (pH 6.0-1.85) on sulfate removal and microbial communities. The optimum <span><math><mrow><mtext>COD</mtext><mo>/</mo><msubsup><mtext>SO</mtext><mn>4</mn><mrow><mn>2</mn><mo>‐</mo></mrow></msubsup></mrow></math></span> ratio and HRT were found to be 0.7 and 4 days, respectively. The SmBR achieved a sulfate and COD removal of 80 % and 87 %, respectively, with an influent sulfate concentration of 4500 mg/L and a <span><math><mrow><mtext>COD</mtext><mo>/</mo><msubsup><mtext>SO</mtext><mn>4</mn><mrow><mn>2</mn><mo>‐</mo></mrow></msubsup></mrow></math></span> ratio of 0.7, and the effluent pH increased from 2.0 to 7.2. Further decreasing the feed pH to 1.85 resulted in a sharp decline in the reactor performance, which was recovered within 30 days by adjusting operational conditions. Electron flow from lactate to sulfate reduction varied between 86 % and 91 %, demonstrating the effective utilization of substrate. 16S rRNA sequencing revealed that the decrease in influent pH from 6.0 to 2.5 led to a shift in microbial diversity towards a specialized group of SRB, particularly <em>Desulfobacterota (Desulfovibrio genus),</em> which increased from 12 to 45 %, emphasizing their crucial role in sulfate removal. The mixed bacterial culture developed in the SmBR could be suitable for treating industrial sulfate-laden acidic wastewaters such as acid mine drainage, lead acid battery manufacturing wastewater, and secondary lead smelting plant wastewater. The findings of this study offer a sustainable bioremediation approach for treating sulfate-laden acidic wastewater.</div></div>","PeriodicalId":13643,"journal":{"name":"International Biodeterioration & Biodegradation","volume":"209 ","pages":"Article 106276"},"PeriodicalIF":4.1,"publicationDate":"2026-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145922623","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 : 2025-12-31DOI: 10.1016/j.ibiod.2025.106274
Zhiman Lin , Jinfan Zhang , Ru Wang , Jingmin Ou , He Zhang , Zihua Wang , Fangyuan Zheng , Xiantao Sun , Xin Wei , Yiming Huang , Zhenguo Chen , Mark C.M. van Loosdrecht , Yuchun Yang
Wastewater treatment is a major source of global greenhouse gas (GHG) emissions, largely driven by nitrous oxide (N2O) release during nitrogen removal processes. While anaerobic ammonium-oxidizing (anammox) bacteria have become widely adopted to optimize nitrogen removal, the pathways governing N2O emissions in anammox systems remain insufficiently characterized. Findings revealed that in aerobic environments with low dissolved oxygen, nitrifying microorganisms showed pronounced upregulation of N2O synthesis genes, confirming their pivotal role in emissions. Conversely, heterotrophic denitrification dominated N2O production in anaerobic systems. Crucially, anammox-dominated biofilms displayed substantially lower expression of N2O-related genes compared to suspended sludge, suggesting reduced emission risks in biofilm configurations. Batch experiments demonstrated a 2.78-fold lower N2O release from biofilms than suspended biomass. This mitigation was linked to restricted substrate transport within biofilms, which curbed NO2− buildup and subsequently suppressed nitrifier-derived N2O formation. Additionally, the high-density colonization of anammox bacteria in biofilms efficient scavenging of nitric oxide (NO) and hydroxylamine (NH2OH), critical intermediates in N2O synthesis. Employing an integrated multi-omics approach, this study investigates N2O production and consumption pathways in diverse anammox systems and unveils the N2O mitigation mechanisms of biofilms, offering fundamental insights for reducing N2O emissions in wastewater treatment.
{"title":"Biofilm-mediated mitigation of nitrous oxide emissions in anammox-based wastewater treatment","authors":"Zhiman Lin , Jinfan Zhang , Ru Wang , Jingmin Ou , He Zhang , Zihua Wang , Fangyuan Zheng , Xiantao Sun , Xin Wei , Yiming Huang , Zhenguo Chen , Mark C.M. van Loosdrecht , Yuchun Yang","doi":"10.1016/j.ibiod.2025.106274","DOIUrl":"10.1016/j.ibiod.2025.106274","url":null,"abstract":"<div><div>Wastewater treatment is a major source of global greenhouse gas (GHG) emissions, largely driven by nitrous oxide (N<sub>2</sub>O) release during nitrogen removal processes. While anaerobic ammonium-oxidizing (anammox) bacteria have become widely adopted to optimize nitrogen removal, the pathways governing N<sub>2</sub>O emissions in anammox systems remain insufficiently characterized. Findings revealed that in aerobic environments with low dissolved oxygen, nitrifying microorganisms showed pronounced upregulation of N<sub>2</sub>O synthesis genes, confirming their pivotal role in emissions. Conversely, heterotrophic denitrification dominated N<sub>2</sub>O production in anaerobic systems. Crucially, anammox-dominated biofilms displayed substantially lower expression of N<sub>2</sub>O-related genes compared to suspended sludge, suggesting reduced emission risks in biofilm configurations. Batch experiments demonstrated a 2.78-fold lower N<sub>2</sub>O release from biofilms than suspended biomass. This mitigation was linked to restricted substrate transport within biofilms, which curbed NO<sub>2</sub><sup>−</sup> buildup and subsequently suppressed nitrifier-derived N<sub>2</sub>O formation. Additionally, the high-density colonization of anammox bacteria in biofilms efficient scavenging of nitric oxide (NO) and hydroxylamine (NH<sub>2</sub>OH), critical intermediates in N<sub>2</sub>O synthesis. Employing an integrated multi-omics approach, this study investigates N<sub>2</sub>O production and consumption pathways in diverse anammox systems and unveils the N<sub>2</sub>O mitigation mechanisms of biofilms, offering fundamental insights for reducing N<sub>2</sub>O emissions in wastewater treatment.</div></div>","PeriodicalId":13643,"journal":{"name":"International Biodeterioration & Biodegradation","volume":"208 ","pages":"Article 106274"},"PeriodicalIF":4.1,"publicationDate":"2025-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145880009","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 : 2025-12-31DOI: 10.1016/j.ibiod.2025.106275
Giovana Manzini , Giuseppe Ciaramella Moita , Romildo Dias Toledo Filho , Eliana Flávia Camporese Sérvulo , Vitor Liduino
This study advances microbial-induced calcium carbonate precipitation (MICP), a technology with potential to mitigate carbon emissions. A composite mixture of natural and recycled stone aggregates was tested for the isolation of carbonate-forming fungi, seeking to explore alternative eukaryotic microorganisms capable of MICP. Three yeast and seven mold cultures were isolated. The yeast isolates, identified through ITS sequencing as Candida orthopsilosis, Naganishia sp., and Rhodotorula mucilaginosa, were evaluated for their ability to produce CaCO3 in an acetate-based medium over a 7-day cultivation period. All three yeasts generated mineral residues, showing different overall yields (ranging from 0.6 to 1.6 g) but with similar carbonate contents (∼20 % as CaCO3). Fourier-transform infrared spectroscopy (FTIR) confirmed the presence of carbonate groups in all mineralized residues. At the same time, thermogravimetric (TG-DTG) analyses revealed that among the isolates, R. mucilaginosa achieved the highest conversion rate of calcium acetate to CaCO3 (48.8 ± 3.1 %), corresponding to a precipitation yield of 0.29 g CaCO3, more than twice that obtained for the other isolates. X-ray diffraction (XRD) analyses revealed that the only CaCO3 polymorph formed was vaterite. These findings provide new insights into the biomineralization capacity of non-ureolytic yeasts and highlight their potential applicability as alternative biocatalysts in MICP-based technologies.
{"title":"Exploring calcium carbonate biomineralization by yeasts isolated from cement-associated environments","authors":"Giovana Manzini , Giuseppe Ciaramella Moita , Romildo Dias Toledo Filho , Eliana Flávia Camporese Sérvulo , Vitor Liduino","doi":"10.1016/j.ibiod.2025.106275","DOIUrl":"10.1016/j.ibiod.2025.106275","url":null,"abstract":"<div><div>This study advances microbial-induced calcium carbonate precipitation (MICP), a technology with potential to mitigate carbon emissions. A composite mixture of natural and recycled stone aggregates was tested for the isolation of carbonate-forming fungi, seeking to explore alternative eukaryotic microorganisms capable of MICP. Three yeast and seven mold cultures were isolated. The yeast isolates, identified through ITS sequencing as <em>Candida orthopsilosis</em>, <em>Naganishia</em> sp., and <em>Rhodotorula mucilaginosa</em>, were evaluated for their ability to produce CaCO<sub>3</sub> in an acetate-based medium over a 7-day cultivation period. All three yeasts generated mineral residues, showing different overall yields (ranging from 0.6 to 1.6 g) but with similar carbonate contents (∼20 % as CaCO<sub>3</sub>). Fourier-transform infrared spectroscopy (FTIR) confirmed the presence of carbonate groups in all mineralized residues. At the same time, thermogravimetric (TG-DTG) analyses revealed that among the isolates, <em>R. mucilaginosa</em> achieved the highest conversion rate of calcium acetate to CaCO<sub>3</sub> (48.8 ± 3.1 %), corresponding to a precipitation yield of 0.29 g CaCO<sub>3</sub>, more than twice that obtained for the other isolates. X-ray diffraction (XRD) analyses revealed that the only CaCO<sub>3</sub> polymorph formed was vaterite. These findings provide new insights into the biomineralization capacity of non-ureolytic yeasts and highlight their potential applicability as alternative biocatalysts in MICP-based technologies.</div></div>","PeriodicalId":13643,"journal":{"name":"International Biodeterioration & Biodegradation","volume":"209 ","pages":"Article 106275"},"PeriodicalIF":4.1,"publicationDate":"2025-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145872364","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 : 2025-12-30DOI: 10.1016/j.ibiod.2025.106273
Hui Li , Zeyu Pan , Chuan Yang , Meng Sun , Hui Jiang , Buyu Cao , Xingxia Ma
This study aimed to evaluate the disinfection effectiveness of ethylene oxide fumigation (EOF) on unearthed wooden cultural relics, with offering practical references for the selection of more comprehensive protection strategies for wood. Two ancient wooden wells from the Beijing Lu County Gucheng ruins park were treated with EOF. Wood species were identified, and rotten wood was observed microscopically. Microbial communities were analyzed through tissue isolation and high-throughput sequencing. Growth characteristics, lignocellulose-degrading enzyme activities, and microbial interactions of isolated strains were further assessed. Enzymatic analyses showed that most isolates lacked ligninolytic activity but exhibited cellulase activity, consistent with soft-rot patterns observed in the wooden wells. Before fumigation, fourteen fungal species were isolated, with Exophiala and Anthracobia dominating. After EOF treatment, only five fungal species were isolated, indicating a substantial reduction in microbial diversity. EOF reduced surface fungal loads but did not fully eliminate deeply invasive strains. These findings indicate the limited sterilization capacity of EOF for archaeological wood, for which improved or complementary disinfection strategies may be required to ensure the long-term preservation of deeply deteriorated wooden cultural relics.
{"title":"Study on the effect of ethylene oxide fumigation on the colonies of unearthed wooden cultural relics","authors":"Hui Li , Zeyu Pan , Chuan Yang , Meng Sun , Hui Jiang , Buyu Cao , Xingxia Ma","doi":"10.1016/j.ibiod.2025.106273","DOIUrl":"10.1016/j.ibiod.2025.106273","url":null,"abstract":"<div><div>This study aimed to evaluate the disinfection effectiveness of ethylene oxide fumigation (EOF) on unearthed wooden cultural relics, with offering practical references for the selection of more comprehensive protection strategies for wood. Two ancient wooden wells from the Beijing Lu County Gucheng ruins park were treated with EOF. Wood species were identified, and rotten wood was observed microscopically. Microbial communities were analyzed through tissue isolation and high-throughput sequencing. Growth characteristics, lignocellulose-degrading enzyme activities, and microbial interactions of isolated strains were further assessed. Enzymatic analyses showed that most isolates lacked ligninolytic activity but exhibited cellulase activity, consistent with soft-rot patterns observed in the wooden wells. Before fumigation, fourteen fungal species were isolated, with <em>Exophiala</em> and <em>Anthracobia</em> dominating. After EOF treatment, only five fungal species were isolated, indicating a substantial reduction in microbial diversity. EOF reduced surface fungal loads but did not fully eliminate deeply invasive strains. These findings indicate the limited sterilization capacity of EOF for archaeological wood, for which improved or complementary disinfection strategies may be required to ensure the long-term preservation of deeply deteriorated wooden cultural relics.</div></div>","PeriodicalId":13643,"journal":{"name":"International Biodeterioration & Biodegradation","volume":"208 ","pages":"Article 106273"},"PeriodicalIF":4.1,"publicationDate":"2025-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145880008","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}
Pseudomonas aeruginosa is a notorious opportunistic pathogenic Gram-negative bacterium, and its virulence and persistence are mainly facilitated by quorum sensing (QS) and biofilm formation. Targeting these mechanisms presents a promising strategy to reduce pathogenicity without exerting selective pressure on bacterial survival. This study examined the anti-virulence potential of Piperonyl alcohol (PAL) against P. aeruginosa PAO1 using both experimental and computational approaches. Our findings revealed that PAL treatment notable decreased the production of key virulence factors, including pyocyanin (72.66 %), total protease (74.66 %), alginate (66.95 %), exopolysaccharides (79.14 %), pyoverdine (79.92 %), and pyochelin (68.28 %). Additionally, biofilm formation was reduced by 83.71 %, which was further validated through catheter-based biofilm assays and microscopic analyses. PAL also impaired swimming, swarming, and twitching motilities, indicating its interference in the initial biofilm formation. Gene expression profiling confirmed the downregulation of major QS regulators (lasR, rhlR, pqsR) and related virulence genes. In silico studies, revealed stable binding of PAL to LasR, RhlR, and PqsR as evidenced by favorable docking scores and corroborated by molecular dynamics simulations. Pharmacokinetic predictions indicated good oral bioavailability and intestinal absorption with no apparent toxicity. In vivo validation using infection models in C. elegans and G. mellonella demonstrated enhanced host survival and reduced pathogen burden. These findings position PAL as a potential QS and biofilm inhibitory agent, with substantial potential for therapeutic management of P. aeruginosa infections.
{"title":"Quorum sensing inhibitory and anti-infective potential of piperonyl alcohol against Pseudomonas aeruginosa","authors":"Paramita Pakhira , Paramanantham Parasuraman , Sampathkumar Ranganathan , Jung-Kul Lee , Mahesh Ramatchandirane , Kitlangki Suchiang , Siddhardha Busi","doi":"10.1016/j.ibiod.2025.106272","DOIUrl":"10.1016/j.ibiod.2025.106272","url":null,"abstract":"<div><div><em>Pseudomonas aeruginosa</em> is a notorious opportunistic pathogenic Gram-negative bacterium, and its virulence and persistence are mainly facilitated by quorum sensing (QS) and biofilm formation. Targeting these mechanisms presents a promising strategy to reduce pathogenicity without exerting selective pressure on bacterial survival. This study examined the anti-virulence potential of Piperonyl alcohol (PAL) against <em>P. aeruginosa</em> PAO1 using both experimental and computational approaches. Our findings revealed that PAL treatment notable decreased the production of key virulence factors, including pyocyanin (72.66 %), total protease (74.66 %), alginate (66.95 %), exopolysaccharides (79.14 %), pyoverdine (79.92 %), and pyochelin (68.28 %). Additionally, biofilm formation was reduced by 83.71 %, which was further validated through catheter-based biofilm assays and microscopic analyses. PAL also impaired swimming, swarming, and twitching motilities, indicating its interference in the initial biofilm formation. Gene expression profiling confirmed the downregulation of major QS regulators (<em>lasR</em>, <em>rhlR</em>, <em>pqsR</em>) and related virulence genes. <em>In silico</em> studies, revealed stable binding of PAL to LasR, RhlR, and PqsR as evidenced by favorable docking scores and corroborated by molecular dynamics simulations. Pharmacokinetic predictions indicated good oral bioavailability and intestinal absorption with no apparent toxicity. <em>In vivo</em> validation using infection models in <em>C. elegans</em> and <em>G. mellonella</em> demonstrated enhanced host survival and reduced pathogen burden. These findings position PAL as a potential QS and biofilm inhibitory agent, with substantial potential for therapeutic management of <em>P. aeruginosa</em> infections.</div></div>","PeriodicalId":13643,"journal":{"name":"International Biodeterioration & Biodegradation","volume":"208 ","pages":"Article 106272"},"PeriodicalIF":4.1,"publicationDate":"2025-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145837080","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 : 2025-12-23DOI: 10.1016/j.ibiod.2025.106270
Qing-Ping He , Yi-Fan Liu , Bo-Wen Wang , Lei Zhou , Shi-Zhong Yang , Ji-Dong Gu , Bo-Zhong Mu
Bathyarchaeia, among the most ubiquitous and abundant microorganisms in nature, play pivotal roles in global carbon cycling. While efforts on their enrichment, classification, genomic, and transcriptomic profiles have been extensively made, pure culture or co-culture with highly enriched Bathyarchaeia remains challenging, particularly in subsurface ecosystems like oil reservoirs. Here, we present a systematic workflow that integrated the Hungate roll-tube technique with 16S rRNA gene amplicon sequencing of total biomass to evaluate cultivation outcomes and identify optimal conditions for Bathyarchaeia by analyzing substrates and temperatures. Under cultivation conditions with various methoxylated aromatic substrates (lignin, syringaldehyde, vanillin, and 3,4,5-trimethoxybenzoate) and three temperatures, this approach led to the successful acquisition of 45 co-cultures containing Bathyarchaeia. Phylogenetic analysis revealed that all recovered Bathyarchaeia operational taxonomic units belonged to subgroup Bathy-6. Co-occurrence network analysis and cultivation results suggested mutualistic interactions between Bathy-6, specific bacterial partners (genus Coprothermobacter, genus Desulfocurvibacter, genus Thermotoga, genus Biomaibacter and genus Thermodesulfovibrio), and methanogens (genus Methanothermobacter, genus Methanothrix and genus Ca. Methanomethylicus) during the degradation of methoxylated aromatics. The optimal cultivation condition for Bathy-6 was determined to be 46 °C with syringaldehyde as the substrate. Furthermore, a novel and efficient DNA extraction protocol from gellan gum-embedded biomass was developed using sodium citrate acidification. Our study provides a effective cultivation strategy for accessing the cryptic Bathyarchaeia and yields a valuable repository of co-cultures. These findings significantly advance our comprehension of the metabolic capabilities and mutualistic lifestyle of Bathyarchaeia in the anaerobic degradation of aromatic compounds within oil reservoir ecosystems.
{"title":"Enrichment and cultivation of thermophilic Bathyarchaeia from oil reservoirs via systematic cultivation profiling","authors":"Qing-Ping He , Yi-Fan Liu , Bo-Wen Wang , Lei Zhou , Shi-Zhong Yang , Ji-Dong Gu , Bo-Zhong Mu","doi":"10.1016/j.ibiod.2025.106270","DOIUrl":"10.1016/j.ibiod.2025.106270","url":null,"abstract":"<div><div>Bathyarchaeia, among the most ubiquitous and abundant microorganisms in nature, play pivotal roles in global carbon cycling. While efforts on their enrichment, classification, genomic, and transcriptomic profiles have been extensively made, pure culture or co-culture with highly enriched <em>Bathyarchaeia</em> remains challenging, particularly in subsurface ecosystems like oil reservoirs. Here, we present a systematic workflow that integrated the Hungate roll-tube technique with 16S rRNA gene amplicon sequencing of total biomass to evaluate cultivation outcomes and identify optimal conditions for <em>Bathyarchaeia</em> by analyzing substrates and temperatures. Under cultivation conditions with various methoxylated aromatic substrates (lignin, syringaldehyde, vanillin, and 3,4,5-trimethoxybenzoate) and three temperatures, this approach led to the successful acquisition of 45 co-cultures containing <em>Bathyarchaeia</em>. Phylogenetic analysis revealed that all recovered <em>Bathyarchaeia</em> operational taxonomic units belonged to subgroup Bathy-6. Co-occurrence network analysis and cultivation results suggested mutualistic interactions between Bathy-6, specific bacterial partners (genus <em>Coprothermobacter</em>, genus <em>Desulfocurvibacter</em>, genus <em>Thermotoga</em>, genus <em>Biomaibacter</em> and genus <em>Thermodesulfovibrio</em>), and methanogens (genus <em>Methanothermobacter</em>, genus <em>Methanothrix</em> and genus <em>Ca.</em> Methanomethylicus) during the degradation of methoxylated aromatics. The optimal cultivation condition for Bathy-6 was determined to be 46 °C with syringaldehyde as the substrate. Furthermore, a novel and efficient DNA extraction protocol from gellan gum-embedded biomass was developed using sodium citrate acidification. Our study provides a effective cultivation strategy for accessing the cryptic <em>Bathyarchaeia</em> and yields a valuable repository of co-cultures. These findings significantly advance our comprehension of the metabolic capabilities and mutualistic lifestyle of <em>Bathyarchaeia</em> in the anaerobic degradation of aromatic compounds within oil reservoir ecosystems.</div></div>","PeriodicalId":13643,"journal":{"name":"International Biodeterioration & Biodegradation","volume":"208 ","pages":"Article 106270"},"PeriodicalIF":4.1,"publicationDate":"2025-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145837079","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 : 2025-12-22DOI: 10.1016/j.ibiod.2025.106271
Ahmet Yazıcıoğlu, Sławomir Ciesielski
Polycyclic aromatic hydrocarbons (PAHs) are still important pollutants in environmental health due to intensive anthropogenic activities and natural disasters. Since PAHs are found in mixed forms with other pollutants in real environment, the search for effective and sustainable PAHs removal methods has become a hot issue in this field. The use of biosurfactants in PAHs biodegradation plays a critical role by decreasing surface tension and increasing bioavailability. However, the exact molecular mechanisms and functional relationships between biosurfactants and PAHs are still poorly understood. This review addresses this significant knowledge gap and systematically examines the current strategies to enhance bioprocess efficiency. We propose an innovative synergy between mechanistic biosurfactant research and predictive machine learning approaches. Particularly, we emphasize the application of large language models (LLMs) in clarifying complicated biosurfactant-PAHs interactions. Through the integration of experimental data with LLM-based interaction modeling, we present a forward-looking perspective on how these technologies can accelerate rational biosurfactant design and optimize remediation strategies. We also bring to the environmental engineering community's attention the essential need for curated datasets, benchmarks, and custom models for the successful integration of this technology into bioremediation applications.
{"title":"Polycyclic aromatic hydrocarbons removal: emerging challenges and innovative solutions","authors":"Ahmet Yazıcıoğlu, Sławomir Ciesielski","doi":"10.1016/j.ibiod.2025.106271","DOIUrl":"10.1016/j.ibiod.2025.106271","url":null,"abstract":"<div><div>Polycyclic aromatic hydrocarbons (PAHs) are still important pollutants in environmental health due to intensive anthropogenic activities and natural disasters. Since PAHs are found in mixed forms with other pollutants in real environment, the search for effective and sustainable PAHs removal methods has become a hot issue in this field. The use of biosurfactants in PAHs biodegradation plays a critical role by decreasing surface tension and increasing bioavailability. However, the exact molecular mechanisms and functional relationships between biosurfactants and PAHs are still poorly understood. This review addresses this significant knowledge gap and systematically examines the current strategies to enhance bioprocess efficiency. We propose an innovative synergy between mechanistic biosurfactant research and predictive machine learning approaches. Particularly, we emphasize the application of large language models (LLMs) in clarifying complicated biosurfactant-PAHs interactions. Through the integration of experimental data with LLM-based interaction modeling, we present a forward-looking perspective on how these technologies can accelerate rational biosurfactant design and optimize remediation strategies. We also bring to the environmental engineering community's attention the essential need for curated datasets, benchmarks, and custom models for the successful integration of this technology into bioremediation applications.</div></div>","PeriodicalId":13643,"journal":{"name":"International Biodeterioration & Biodegradation","volume":"208 ","pages":"Article 106271"},"PeriodicalIF":4.1,"publicationDate":"2025-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145837078","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}
Buried timber piles play a critical role in ground improvement, yet their long-term deterioration under waterlogged and anaerobic conditions remains insufficiently understood. This study investigated microbial communities and wood degradation in Japanese cedar (Cryptomeria japonica) and Japanese larch (Larix kaempferi) logs used for ground improvement, a geotechnical method that stabilizes soft or liquefiable soils. The logs were buried for 8–10 years at two sites with differing soil compositions and groundwater conditions. Bacterial communities were analyzed using next-generation sequencing (NGS). In cedar, bacterial infiltration extended from the outermost sapwood to the inner sapwood and into the heartwood, likely due to its lower density and higher water permeability. In contrast, bacterial colonization in larch was confined primarily to the outermost sapwood, likely reflecting its higher density and lower permeability. Microscopic analysis revealed erosion of parenchyma cell walls in cedar and slight deterioration of tracheid cell walls in larch, but no apparent reduction in wood density was observed. Dominant bacterial taxa included the anaerobic classes Clostridia and Limnochordia in cedar, and Clostridia and Negativicutes in larch. Facultative anaerobes dominated the surrounding soil, particularly members of the order Chitinophagales. These findings suggest that initial bacterial colonization of the logs was influenced by the soil microbiota and subsequently shaped by their internal environmental conditions. Although fungal communities were identified by ITS amplicon analysis and microscopic observation of cell walls, no apparent signs of fungal degradation were observed. Overall, the results underscore the importance of wood density and permeability in microbial resistance, with larch exhibiting greater durability under anaerobic soil conditions. This study contributes to a deeper understanding of the long-term stability of buried wood in geotechnical applications.
{"title":"Wood deterioration assessment and microbial community analysis of foundation piles experimentally installed for 8 and 10 years","authors":"Sitompul Afrida , Ikuo Momohara , Yuka Miyoshi , Takumi Murata , Atsunori Numata , Sakae Horisawa","doi":"10.1016/j.ibiod.2025.106269","DOIUrl":"10.1016/j.ibiod.2025.106269","url":null,"abstract":"<div><div>Buried timber piles play a critical role in ground improvement, yet their long-term deterioration under waterlogged and anaerobic conditions remains insufficiently understood. This study investigated microbial communities and wood degradation in Japanese cedar (<em>Cryptomeria japonica</em>) and Japanese larch (<em>Larix kaempferi</em>) logs used for ground improvement, a geotechnical method that stabilizes soft or liquefiable soils. The logs were buried for 8–10 years at two sites with differing soil compositions and groundwater conditions. Bacterial communities were analyzed using next-generation sequencing (NGS). In cedar, bacterial infiltration extended from the outermost sapwood to the inner sapwood and into the heartwood, likely due to its lower density and higher water permeability. In contrast, bacterial colonization in larch was confined primarily to the outermost sapwood, likely reflecting its higher density and lower permeability. Microscopic analysis revealed erosion of parenchyma cell walls in cedar and slight deterioration of tracheid cell walls in larch, but no apparent reduction in wood density was observed. Dominant bacterial taxa included the anaerobic classes <em>Clostridia</em> and <em>Limnochordia</em> in cedar, and <em>Clostridia</em> and <em>Negativicutes</em> in larch. Facultative anaerobes dominated the surrounding soil, particularly members of the order <em>Chitinophagales</em>. These findings suggest that initial bacterial colonization of the logs was influenced by the soil microbiota and subsequently shaped by their internal environmental conditions. Although fungal communities were identified by ITS amplicon analysis and microscopic observation of cell walls, no apparent signs of fungal degradation were observed. Overall, the results underscore the importance of wood density and permeability in microbial resistance, with larch exhibiting greater durability under anaerobic soil conditions. This study contributes to a deeper understanding of the long-term stability of buried wood in geotechnical applications.</div></div>","PeriodicalId":13643,"journal":{"name":"International Biodeterioration & Biodegradation","volume":"208 ","pages":"Article 106269"},"PeriodicalIF":4.1,"publicationDate":"2025-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145797491","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 : 2025-12-11DOI: 10.1016/j.ibiod.2025.106268
Carlos Esteven Pulgarín-Muñoz , Julio César Saldarriaga-Molina , José Francisco Molina-Pérez , Daniela Gonzalez-Pantoja , Lina María Goez-Gaviria
The increasing production of sewage sludge from the cosmetic industry, driven by the sector's continuous growth, has created a pressing need for sustainable treatment and valorization alternatives. These sludges are often complex and challenging to treat due to their physicochemical composition and potential environmental risks. This study evaluates the methane production potential of anaerobic mono-digestion (AMoD) and anaerobic co-digestion (ACoD) of cosmetic industry sewage sludge (CSS) with the organic fraction of municipal solid waste (OFMSW). Four experimental configurations were established with CSS:OFMSW substrate ratios of 100/0, 70/30, 50/50, and 30/70. The results show that increasing the proportion of OFMSW significantly enhances methane production, with the highest yield observed at the 30:70 ratio. The synergistic effect of ACoD was assessed using the Co-Digestion Performance Index (CPI), which indicated a synergistic interaction when the OFMSW proportion exceeded 50 %. Six kinetic models were applied, among which the Modified Gompertz model best described AMoD and ACoD at 70:30 and 50:50 ratios, while the Cone model more accurately represented the system at the 30:70 ratio. This study demonstrates the feasibility of treating CSS through anaerobic digestion and highlights that co-digestion with OFMSW can optimize biogas production, promote sustainable waste management, and enable the valorization of both industrial and municipal organic residues.
{"title":"Anaerobic mono and co-digestion of cosmetic sewage sludge and organic fraction of municipal solid waste: Methane yield and kinetic modeling","authors":"Carlos Esteven Pulgarín-Muñoz , Julio César Saldarriaga-Molina , José Francisco Molina-Pérez , Daniela Gonzalez-Pantoja , Lina María Goez-Gaviria","doi":"10.1016/j.ibiod.2025.106268","DOIUrl":"10.1016/j.ibiod.2025.106268","url":null,"abstract":"<div><div>The increasing production of sewage sludge from the cosmetic industry, driven by the sector's continuous growth, has created a pressing need for sustainable treatment and valorization alternatives. These sludges are often complex and challenging to treat due to their physicochemical composition and potential environmental risks. This study evaluates the methane production potential of anaerobic mono-digestion (AMoD) and anaerobic co-digestion (ACoD) of cosmetic industry sewage sludge (CSS) with the organic fraction of municipal solid waste (OFMSW). Four experimental configurations were established with CSS:OFMSW substrate ratios of 100/0, 70/30, 50/50, and 30/70. The results show that increasing the proportion of OFMSW significantly enhances methane production, with the highest yield observed at the 30:70 ratio. The synergistic effect of ACoD was assessed using the Co-Digestion Performance Index (CPI), which indicated a synergistic interaction when the OFMSW proportion exceeded 50 %. Six kinetic models were applied, among which the Modified Gompertz model best described AMoD and ACoD at 70:30 and 50:50 ratios, while the Cone model more accurately represented the system at the 30:70 ratio. This study demonstrates the feasibility of treating CSS through anaerobic digestion and highlights that co-digestion with OFMSW can optimize biogas production, promote sustainable waste management, and enable the valorization of both industrial and municipal organic residues.</div></div>","PeriodicalId":13643,"journal":{"name":"International Biodeterioration & Biodegradation","volume":"208 ","pages":"Article 106268"},"PeriodicalIF":4.1,"publicationDate":"2025-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145748553","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 : 2025-12-10DOI: 10.1016/j.ibiod.2025.106257
Clotilde Maestri , Alexis Duthoit , Ronan L. Hébert , Laure Bredif , Patrick Di Martino
This study investigates the biodeterioration potential of the polyurethane waterproofing coating PU 636 by Aspergillus niger ERAN01 under in vitro conditions. Two protocols, adapted from the ISO 846 standard, were employed using agar media with different nutrient contents. After 9 weeks of incubation at 27 °C and 80 % relative humidity, macroscopic, microscopic, mechanical, and spectroscopic analyses were conducted to assess biodeterioration. Fungal colonization was more extensive in the presence of glucose, which correlated with visible colour changes (notably yellowing), a statistically significant increase in surface roughness, the formation of surface cavities observed via scanning electron microscopy, and chemical modifications detected through infrared spectroscopy. Signs of hydrolysis of ester and urethane bonds, as well as oxidation of ether linkages were observed. Despite these changes, tensile strength measurements showed no significant degradation of the material's mechanical integrity. The results suggest that A. niger produces hydrolases and metabolites capable of inducing greater physical and chemical deterioration of polyurethane coating in the presence of glucose. This study emphasizes the importance of environmental conditions, particularly nutrient availability, in influencing fungal biodeterioration of polymeric materials and supports the need for adapted methodologies when evaluating the biodeterioration of polyurethane waterproofing coatings.
{"title":"Biodeterioration of a polyurethane topcoat by Aspergillus niger","authors":"Clotilde Maestri , Alexis Duthoit , Ronan L. Hébert , Laure Bredif , Patrick Di Martino","doi":"10.1016/j.ibiod.2025.106257","DOIUrl":"10.1016/j.ibiod.2025.106257","url":null,"abstract":"<div><div>This study investigates the biodeterioration potential of the polyurethane waterproofing coating PU 636 by <em>Aspergillus niger</em> ERAN01 under <em>in vitro</em> conditions. Two protocols, adapted from the ISO 846 standard, were employed using agar media with different nutrient contents. After 9 weeks of incubation at 27 °C and 80 % relative humidity, macroscopic, microscopic, mechanical, and spectroscopic analyses were conducted to assess biodeterioration. Fungal colonization was more extensive in the presence of glucose, which correlated with visible colour changes (notably yellowing), a statistically significant increase in surface roughness, the formation of surface cavities observed via scanning electron microscopy, and chemical modifications detected through infrared spectroscopy. Signs of hydrolysis of ester and urethane bonds, as well as oxidation of ether linkages were observed. Despite these changes, tensile strength measurements showed no significant degradation of the material's mechanical integrity. The results suggest that <em>A. niger</em> produces hydrolases and metabolites capable of inducing greater physical and chemical deterioration of polyurethane coating in the presence of glucose. This study emphasizes the importance of environmental conditions, particularly nutrient availability, in influencing fungal biodeterioration of polymeric materials and supports the need for adapted methodologies when evaluating the biodeterioration of polyurethane waterproofing coatings.</div></div>","PeriodicalId":13643,"journal":{"name":"International Biodeterioration & Biodegradation","volume":"208 ","pages":"Article 106257"},"PeriodicalIF":4.1,"publicationDate":"2025-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145748554","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}