International Biodeterioration & Biodegradation最新文献_第3页

Polycyclic aromatic hydrocarbons removal: emerging challenges and innovative solutions 多环芳烃去除：新出现的挑战和创新的解决方案

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

International Biodeterioration & Biodegradation

Pub Date : 2025-12-22 DOI: 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.

由于人类活动和自然灾害的频繁，多环芳烃（PAHs）仍然是影响环境健康的重要污染物。由于多环芳烃在现实环境中与其他污染物以混合形式存在，寻找有效、可持续的多环芳烃去除方法已成为该领域的热点问题。生物表面活性剂在多环芳烃生物降解中起着降低表面张力和提高生物利用度的关键作用。然而，生物表面活性剂与多环芳烃之间的确切分子机制和功能关系仍然知之甚少。这篇综述解决了这一重要的知识差距，并系统地检查了提高生物过程效率的当前策略。我们提出了机械生物表面活性剂研究和预测机器学习方法之间的创新协同作用。特别地，我们强调大语言模型（LLMs）在阐明复杂的生物表面活性剂-多环芳烃相互作用中的应用。通过将实验数据与基于llm的相互作用建模相结合，我们提出了这些技术如何加速合理的生物表面活性剂设计和优化修复策略的前瞻性观点。我们也让环境工程界注意到，为了成功地将这项技术整合到生物修复应用中，对精心策划的数据集、基准和定制模型的基本需求。

{"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}

引用次数: 0

Wood deterioration assessment and microbial community analysis of foundation piles experimentally installed for 8 and 10 years 试验安装8年和10年桩基木材劣化评价及微生物群落分析

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

International Biodeterioration & Biodegradation

Pub Date : 2025-12-17 DOI: 10.1016/j.ibiod.2025.106269

Sitompul Afrida , Ikuo Momohara , Yuka Miyoshi , Takumi Murata , Atsunori Numata , Sakae Horisawa

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.

埋地木桩在地基改善中起着至关重要的作用，但其在浸水和厌氧条件下的长期劣化仍未得到充分的了解。本研究调查了日本雪松（Cryptomeria japonica）和日本落叶松（Larix kaempferi）原木的微生物群落和木材退化情况。日本落叶松是一种用于稳定软质或可液化土壤的岩土工程方法。这些原木在两个不同土壤成分和地下水条件的地点埋藏了8-10年。利用下一代测序（NGS）分析细菌群落。在雪松中，细菌的渗透从最外层边材延伸到内部边材，并进入心材，这可能是由于其密度较低，透水性较高。相比之下，落叶松的细菌定植主要局限于最外层的边材，这可能反映了其较高的密度和较低的渗透率。显微分析显示雪松薄壁细胞壁被侵蚀，落叶松管胞细胞壁有轻微退化，但木材密度未见明显下降。优势细菌类群为杉木中的厌氧梭状芽孢杆菌和Limnochordia，落叶松中的梭状芽孢杆菌和阴性芽孢杆菌。兼性厌氧菌在周围土壤中占主导地位，尤其是食几丁菌目的成员。这些发现表明，原木最初的细菌定植受到土壤微生物群的影响，随后受到其内部环境条件的影响。虽然通过ITS扩增子分析和细胞壁的显微镜观察确定了真菌群落，但没有观察到真菌降解的明显迹象。总体而言，结果强调了木材密度和渗透性对微生物抗性的重要性，落叶松在厌氧土壤条件下表现出更强的耐久性。本研究有助于更深入地了解埋地木材在岩土工程应用中的长期稳定性。

{"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}

引用次数: 0

Anaerobic mono and co-digestion of cosmetic sewage sludge and organic fraction of municipal solid waste: Methane yield and kinetic modeling 化妆品污水污泥和城市固体废物有机组分的厌氧单一和共消化：甲烷产量和动力学模型

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

International Biodeterioration & Biodegradation

Pub Date : 2025-12-11 DOI: 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.

在化妆品行业持续增长的推动下，该行业污水污泥的产量不断增加，迫切需要可持续处理和增值替代方案。由于其物理化学成分和潜在的环境风险，这些污泥通常是复杂和具有挑战性的处理。本研究评价了化妆品工业污水污泥（CSS）与城市生活垃圾（OFMSW）有机组分厌氧单消化（AMoD）和厌氧共消化（ACoD）产甲烷的潜力。采用CSS建立了四种实验配置：OFMSW基质比分别为100/0、70/30、50/50和30/70。结果表明：增加OFMSW的添加比例可显著提高甲烷产量，在添加比例为30:70时甲烷产量最高。采用共消化性能指数（CPI）评价ACoD的协同效应，表明当OFMSW的比例超过50%时，ACoD的协同作用存在。采用了6种动力学模型，其中修正的Gompertz模型最能描述70:30和50:50比例下的AMoD和ACoD，而Cone模型更能准确地描述30:70比例下的系统。本研究证明了通过厌氧消化处理CSS的可行性，并强调了与OFMSW共消化可以优化沼气生产，促进废物可持续管理，并实现工业和城市有机残留物的增值。

{"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}

引用次数: 0

Biodeterioration of a polyurethane topcoat by Aspergillus niger 黑曲霉对聚氨酯面漆的生物降解

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

International Biodeterioration & Biodegradation

Pub Date : 2025-12-10 DOI: 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.

研究了黑曲霉ERAN01在体外条件下对聚氨酯防水涂料PU 636的生物降解潜力。采用不同营养成分的琼脂培养基，采用ISO 846标准的两种方案。在27°C和80%相对湿度条件下培养9周后，进行宏观、微观、力学和光谱分析，以评估生物变质情况。在葡萄糖存在的情况下，真菌的定植更广泛，这与可见的颜色变化（特别是变黄）、表面粗糙度的统计显着增加、通过扫描电子显微镜观察到的表面空腔的形成以及通过红外光谱检测到的化学修饰相关。观察到酯和聚氨酯键水解以及醚键氧化的迹象。尽管有这些变化，拉伸强度测量显示材料的机械完整性没有明显的退化。结果表明，在葡萄糖的存在下，黑曲霉产生的水解酶和代谢物能够引起聚氨酯涂层更大的物理和化学劣化。这项研究强调了环境条件的重要性，特别是营养物质的可用性，在影响真菌对聚合物材料的生物降解方面，并支持在评估聚氨酯防水涂料的生物降解时需要适应的方法。

{"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}

引用次数: 0

Elucidating the dual effects of DOM from composted pig manure on Aliinostoc (Cyanobacteria): Convergence of positive and negative impacts 阐明堆肥猪粪DOM对蓝藻的双重影响：正面和负面影响的趋同

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

International Biodeterioration & Biodegradation

Pub Date : 2025-12-08 DOI: 10.1016/j.ibiod.2025.106267

Qiong Yan, Congcong Wang, Yu Shu, Yuexi Jiang, Anwei Chen, Liang Peng, Si Luo, Jihai Shao

The complex composition of dissolved organic matter (DOM) underlies its diverse biological effects on microorganisms. This study investigated the dual positive and negative effects of DOM derived from composted pig manure (CPM-DOM) on the diazotrophic cyanobacterium Aliinostoc sp. YYLX235. Physiological responses, including growth, photosynthesis, N₂-fixation, and antioxidative activity, were evaluated under CPM-DOM exposure (40–240 mg L⁻¹). After 2 days of exposure to CPM-DOM at concentrations ranging from 40 to 240 mg L⁻¹, the growth of Aliinostoc increased by 74.8 %–167.2 %, while its nitrogen-fixation activity was inhibited by 67.0 % and 87.4 % at CPM-DOM concentrations of 160 mg L⁻¹ and 240 mg L⁻¹, respectively. The temporal dynamics of phycobiliprotein content under CPM-DOM exposure exhibited an opposite trend to the electron transport efficiency of photosystem II (PS II). The combined effects of nutrient supplementation and allelopathy likely accounted for the complex physiological responses of Aliinostoc to CPM-DOM exposure. Certain toxic fractions in CPM-DOM, such as cysteinylglycine-containing substances, may bind to nitrogenase and PS II D1 protein, thereby interfering with their functions. CPM-DOM also reduced reactive oxygen species (ROS) and lipid peroxidation, indicating an absence of oxidative stress. These results reveal concentration-dependent trade-offs between growth stimulation and metabolic inhibition, with significant implications for optimizing the co-application of composted pig manure fertilizers and diazotrophic cyanobacteria-based biofertilizers in rice cultivation.

溶解有机物（DOM）的复杂组成决定了其对微生物的多种生物学作用。研究了堆肥猪粪DOM （CPM-DOM）对重氮营养蓝藻Aliinostoc sp. YYLX235的正负双重影响。在CPM-DOM暴露（40-240 mg L−1）条件下，研究了植物的生理反应，包括生长、光合作用、氮固定和抗氧化活性。CPM-DOM浓度为40 ~ 240 mg L−1，处理2 d后，Aliinostoc的生长速度提高了74.8% ~ 167.2%，而固氮活性在CPM-DOM浓度为160 mg L−1和240 mg L−1时分别被抑制了67.0%和87.4%。CPM-DOM暴露下藻胆蛋白含量的时间动态与光系统II （PS II）的电子传递效率呈相反趋势。营养补充和化感作用的联合作用可能解释了Aliinostoc对CPM-DOM暴露的复杂生理反应。CPM-DOM中某些有毒组分，如含半胱氨酸甘氨酸的物质，可能与氮酶和PS II D1蛋白结合，从而干扰其功能。CPM-DOM还能减少活性氧（ROS）和脂质过氧化，表明不存在氧化应激。这些结果揭示了生长刺激和代谢抑制之间的浓度依赖权衡，对优化堆肥猪粪肥料和重氮营养蓝藻生物肥料在水稻栽培中的共同施用具有重要意义。

{"title":"Elucidating the dual effects of DOM from composted pig manure on Aliinostoc (Cyanobacteria): Convergence of positive and negative impacts","authors":"Qiong Yan, Congcong Wang, Yu Shu, Yuexi Jiang, Anwei Chen, Liang Peng, Si Luo, Jihai Shao","doi":"10.1016/j.ibiod.2025.106267","DOIUrl":"10.1016/j.ibiod.2025.106267","url":null,"abstract":"<div><div>The complex composition of dissolved organic matter (DOM) underlies its diverse biological effects on microorganisms. This study investigated the dual positive and negative effects of DOM derived from composted pig manure (CPM-DOM) on the diazotrophic cyanobacterium <em>Aliinostoc</em> sp. YYLX235. Physiological responses, including growth, photosynthesis, N<sub>2</sub>-fixation, and antioxidative activity, were evaluated under CPM-DOM exposure (40–240 mg L<sup>−1</sup>). After 2 days of exposure to CPM-DOM at concentrations ranging from 40 to 240 mg L<sup>−1</sup>, the growth of <em>Aliinostoc</em> increased by 74.8 %–167.2 %, while its nitrogen-fixation activity was inhibited by 67.0 % and 87.4 % at CPM-DOM concentrations of 160 mg L<sup>−1</sup> and 240 mg L<sup>−1</sup>, respectively. The temporal dynamics of phycobiliprotein content under CPM-DOM exposure exhibited an opposite trend to the electron transport efficiency of photosystem II (PS II). The combined effects of nutrient supplementation and allelopathy likely accounted for the complex physiological responses of <em>Aliinostoc</em> to CPM-DOM exposure. Certain toxic fractions in CPM-DOM, such as cysteinylglycine-containing substances, may bind to nitrogenase and PS II D1 protein, thereby interfering with their functions. CPM-DOM also reduced reactive oxygen species (ROS) and lipid peroxidation, indicating an absence of oxidative stress. These results reveal concentration-dependent trade-offs between growth stimulation and metabolic inhibition, with significant implications for optimizing the co-application of composted pig manure fertilizers and diazotrophic cyanobacteria-based biofertilizers in rice cultivation.</div></div>","PeriodicalId":13643,"journal":{"name":"International Biodeterioration & Biodegradation","volume":"208 ","pages":"Article 106267"},"PeriodicalIF":4.1,"publicationDate":"2025-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145748552","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

Temporal metabarcoding of a lignocellulolytic bacterial consortium unveils compositional, structural, and potential functional adaptations 木质纤维素分解细菌联合体的时间元条形码揭示了组成，结构和潜在的功能适应

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

International Biodeterioration & Biodegradation

Pub Date : 2025-12-06 DOI: 10.1016/j.ibiod.2025.106266

Lucas Amoroso Lopes de Carvalho , Anna Carolina de Oliveira Souza , Camila Cesário Fernandes , Eliana Gertrudes de Macedo Lemos , Lúcia Maria Carareto Alves , Daniel Guariz Pinheiro

Lignocellulosic biomass is a key resource for sustainable energy, but its complex structure poses challenges for degradation. Microbial consortia offer a robust solution due to their collective metabolic capabilities; however, understanding their adaptation over time is crucial for optimizing industrial processes. This study investigated the temporal dynamics of a soil-derived bacterial consortium during early (2-week) and late (20-week) stages of exposure to a lignocellulosic substrate. Using 16S rRNA gene metabarcoding, we compared community composition, diversity, and predicted functional profiles across degradation time points (days 0, 5, and 10). Results revealed significant taxonomic shifts, with adaptive stage and degradation day explaining approximately 70 % of community variance (PCoA). Although both stages began with similar ASV richness (early: 287.33 ± 15.01; late: 286.67 ± 37.29), the early stage was characterized by the dominance of a few taxa, whereas the late stage presented greater evenness and a more balanced functional profile. This compositional reorganization occurred alongside a broadly conserved predicted functional potential, with over 96 % of predicted KEGG Orthologs (KOs) shared between stages, suggesting functional redundancy. Despite this conservation, 2215 KOs were differentially abundant, primarily within carbohydrate, amino acid, and xenobiotic metabolism pathways, with nearly 65 % becoming more abundant in the late stage. Our findings demonstrate that while taxonomic composition evolves, the predicted functional potential remains relatively stable, a key trait for developing resilient biotechnological applications.

木质纤维素生物质是可持续能源的关键资源，但其复杂的结构给降解带来了挑战。微生物联合体提供了一个强大的解决方案，由于他们的集体代谢能力；然而，了解它们随时间的适应性对于优化工业过程至关重要。本研究调查了暴露于木质纤维素底物的早期（2周）和后期（20周）土壤来源细菌联合体的时间动态。使用16S rRNA基因元条形码，我们比较了群落组成、多样性，并预测了降解时间点（第0、5和10天）的功能特征。结果显示了显著的分类学变化，适应阶段和退化日解释了大约70%的群落变异（PCoA）。虽然两个阶段的ASV丰富度相似（早期：287.33±15.01；晚期：286.67±37.29），但早期表现为少数类群的优势，而后期则表现出更大的均匀性和更平衡的功能剖面。这种组合重组与广泛保守的预测功能电位一起发生，超过96%的预测KEGG Orthologs （ko）在阶段之间共享，表明功能冗余。尽管存在这种保守性，但2215个KOs的丰度存在差异，主要是在碳水化合物、氨基酸和外源代谢途径中，其中近65%的KOs在后期变得更加丰富。我们的研究结果表明，虽然分类组成不断演变，但预测的功能潜力保持相对稳定，这是开发弹性生物技术应用的关键特征。

{"title":"Temporal metabarcoding of a lignocellulolytic bacterial consortium unveils compositional, structural, and potential functional adaptations","authors":"Lucas Amoroso Lopes de Carvalho , Anna Carolina de Oliveira Souza , Camila Cesário Fernandes , Eliana Gertrudes de Macedo Lemos , Lúcia Maria Carareto Alves , Daniel Guariz Pinheiro","doi":"10.1016/j.ibiod.2025.106266","DOIUrl":"10.1016/j.ibiod.2025.106266","url":null,"abstract":"<div><div>Lignocellulosic biomass is a key resource for sustainable energy, but its complex structure poses challenges for degradation. Microbial consortia offer a robust solution due to their collective metabolic capabilities; however, understanding their adaptation over time is crucial for optimizing industrial processes. This study investigated the temporal dynamics of a soil-derived bacterial consortium during early (2-week) and late (20-week) stages of exposure to a lignocellulosic substrate. Using 16S rRNA gene metabarcoding, we compared community composition, diversity, and predicted functional profiles across degradation time points (days 0, 5, and 10). Results revealed significant taxonomic shifts, with adaptive stage and degradation day explaining approximately 70 % of community variance (PCoA). Although both stages began with similar ASV richness (early: 287.33 ± 15.01; late: 286.67 ± 37.29), the early stage was characterized by the dominance of a few taxa, whereas the late stage presented greater evenness and a more balanced functional profile. This compositional reorganization occurred alongside a broadly conserved predicted functional potential, with over 96 % of predicted KEGG Orthologs (KOs) shared between stages, suggesting functional redundancy. Despite this conservation, 2215 KOs were differentially abundant, primarily within carbohydrate, amino acid, and xenobiotic metabolism pathways, with nearly 65 % becoming more abundant in the late stage. Our findings demonstrate that while taxonomic composition evolves, the predicted functional potential remains relatively stable, a key trait for developing resilient biotechnological applications.</div></div>","PeriodicalId":13643,"journal":{"name":"International Biodeterioration & Biodegradation","volume":"208 ","pages":"Article 106266"},"PeriodicalIF":4.1,"publicationDate":"2025-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145748555","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

Revealing the driving mechanism of efficient microbial degradation of aromatic compounds with phenol as co-substrate from gene transcription level 从基因转录水平揭示以苯酚为共底物的微生物高效降解芳香族化合物的驱动机制

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

International Biodeterioration & Biodegradation

Pub Date : 2025-12-05 DOI: 10.1016/j.ibiod.2025.106265

Xingshe Liu , Qianfeng Yin , Lanxiang Zheng , Haobo He , Xinyun Wang

The excessive content of aromatic compounds was a key factor restricting the difficult discharge of various industrial wastewater. In this study, the microbial enhanced degradation characteristics of aromatic compounds were investigated with naphthalene, phenanthrene, and pyrene were selected as representative, and phenol as co-substrate. Furthermore, the driving mechanisms of microbial-enhanced degradation of aromatic compounds were revealed from the perspectives of enzyme activity and gene transcription levels. The results indicated that the initiation degradation times for naphthalene, phenanthrene, and pyrene were advanced by 4, 6 and 6 h, respectively, with phenol as co-substrate. Correspondingly, the metabolic rates increased by 56.63 %, 46.24 %, and 35.38 %, respectively. Further mechanism analysis showed that the initial dioxygenase NDO (Key enzymes catalyzing the preliminary oxidation of aromatic rings) activity increased by 1.25–1.89 fold and was expressed 12 h earlier due to the co-substrate. The expression of genes ubiH and ygiD encoding the key enzymes 2-octenyl-6-methoxyphenol hydroxylase and 4,5-DOPA exodiol dioxygenase related to degradation initiation was upregulated by 2.25–4.45 fold and 3.04–4.04 fold, respectively. Additionally, the expression of genes encoding key enzymes associated with further ring-opening cleavage—namely aldB, phdI, dmpB, catA, pht3, pht5, and ligA—was significantly upregulated, and the activities of C23O and C21O were markedly enhanced. Additionally, several genes related to carbohydrate, amino acid, and TCA cycle metabolism were found to be upregulated, effectively promoting the cooperation between various metabolic pathways and facilitating ATP synthesis, which provided more energy for microbial metabolism. Therefore, this study provided reliable theoretical basis for efficient degradation of aromatic compounds.

芳香族化合物含量超标是制约各类工业废水难以排放的关键因素。本研究以萘、菲、芘为代表，苯酚为共底物，研究了微生物对芳香族化合物的强化降解特性。此外，从酶活性和基因转录水平等方面揭示了微生物增强芳香族化合物降解的驱动机制。结果表明，以苯酚为共底物时，对萘、菲和芘的起始降解时间分别提前了4、6和6 h。相应的，代谢率分别提高了56.63%、46.24%和35.38%。进一步的机制分析表明，在共底物的作用下，初始双加氧酶NDO（催化芳香环初步氧化的关键酶）活性提高了1.25 ~ 1.89倍，表达时间提前了12 h。编码降解起始相关关键酶2-辛烯基-6-甲氧基酚羟化酶和4,5-多巴外二醇双加氧酶的基因ubiH和ygiD的表达分别上调2.25-4.45倍和3.04-4.04倍。此外，与进一步开环切割相关的关键酶编码基因aldB、phdI、dmpB、catA、pht3、pht5和liga的表达量显著上调，C23O和C21O的活性显著增强。此外，与碳水化合物、氨基酸和TCA循环代谢相关的几个基因被发现上调，有效地促进了各种代谢途径之间的合作，促进了ATP的合成，为微生物代谢提供了更多的能量。本研究为芳香族化合物的高效降解提供了可靠的理论依据。

{"title":"Revealing the driving mechanism of efficient microbial degradation of aromatic compounds with phenol as co-substrate from gene transcription level","authors":"Xingshe Liu , Qianfeng Yin , Lanxiang Zheng , Haobo He , Xinyun Wang","doi":"10.1016/j.ibiod.2025.106265","DOIUrl":"10.1016/j.ibiod.2025.106265","url":null,"abstract":"<div><div>The excessive content of aromatic compounds was a key factor restricting the difficult discharge of various industrial wastewater. In this study, the microbial enhanced degradation characteristics of aromatic compounds were investigated with naphthalene, phenanthrene, and pyrene were selected as representative, and phenol as co-substrate. Furthermore, the driving mechanisms of microbial-enhanced degradation of aromatic compounds were revealed from the perspectives of enzyme activity and gene transcription levels. The results indicated that the initiation degradation times for naphthalene, phenanthrene, and pyrene were advanced by 4, 6 and 6 h, respectively, with phenol as co-substrate. Correspondingly, the metabolic rates increased by 56.63 %, 46.24 %, and 35.38 %, respectively. Further mechanism analysis showed that the initial dioxygenase NDO (Key enzymes catalyzing the preliminary oxidation of aromatic rings) activity increased by 1.25–1.89 fold and was expressed 12 h earlier due to the co-substrate. The expression of genes <em>ubi</em>H and <em>ygi</em>D encoding the key enzymes 2-octenyl-6-methoxyphenol hydroxylase and 4,5-DOPA exodiol dioxygenase related to degradation initiation was upregulated by 2.25–4.45 fold and 3.04–4.04 fold, respectively. Additionally, the expression of genes encoding key enzymes associated with further ring-opening cleavage—namely <em>ald</em>B, <em>phd</em>I, <em>dmp</em>B, <em>cat</em>A, <em>pht</em>3, <em>pht</em>5, and <em>lig</em>A—was significantly upregulated, and the activities of C23O and C21O were markedly enhanced. Additionally, several genes related to carbohydrate, amino acid, and TCA cycle metabolism were found to be upregulated, effectively promoting the cooperation between various metabolic pathways and facilitating ATP synthesis, which provided more energy for microbial metabolism. Therefore, this study provided reliable theoretical basis for efficient degradation of aromatic compounds.</div></div>","PeriodicalId":13643,"journal":{"name":"International Biodeterioration & Biodegradation","volume":"208 ","pages":"Article 106265"},"PeriodicalIF":4.1,"publicationDate":"2025-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145692435","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

Directed mycosorption enhanced by nanopowders: An innovative strategy for eliminating toxic metals during mushroom cultivation 纳米粉末增强的定向真菌吸附：在蘑菇培养过程中消除有毒金属的创新策略

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

International Biodeterioration & Biodegradation

Pub Date : 2025-12-05 DOI: 10.1016/j.ibiod.2025.106253

Agata Krakowska , Małgorzata Suchanek , Ewa Niewiara , Tomasz Skalski , Bożena Muszyńska

This study presents a novel strategy combining the natural metal-accumulating capacity of selected mushrooms with the use of uniquely synthesized nanopowders possessing high sorption properties to achieve targeted mycosorption. Using six mushroom species and six nanopowders, including TiO₂, Fe₂O₃, and yttria-stabilized zirconia (YSZ) variants doped with neodymium, we assessed metal uptake (Mg, Zn, Cd, Pb) and desorption under conditions simulating gastric digestion. Results showed over 90 % accumulation of elements by mushrooms and nanopowders, with nanopowders effectively retaining toxic metals without desorption, thereby reducing their bioavailability in a digestive model. Surface morphology and pore characteristics were analyzed to elucidate sorption efficiency. Our findings demonstrate the potential of combining selective mushroom cultivation with nanopowder application to enhance functional food safety and quality.

本研究提出了一种新的策略，将选定蘑菇的天然金属积累能力与使用独特合成的具有高吸附性能的纳米粉末相结合，以实现靶向真菌吸附。利用六种蘑菇和六种纳米粉末，包括掺杂钕的TiO2、Fe2O3和钇稳定氧化锆（YSZ），我们在模拟胃消化的条件下评估了金属的吸收（Mg、Zn、Cd、Pb）和解吸。结果表明，蘑菇和纳米粉末积累了90%以上的元素，纳米粉末有效地保留了有毒金属而不解吸，从而降低了它们在消化模型中的生物利用度。分析表面形貌和孔隙特征来阐明吸附效率。我们的研究结果表明，将选择性蘑菇培养与纳米粉末应用相结合，可以提高功能性食品的安全性和质量。

引用次数: 0

Resolving the mummification enigma of Baroness Zsófia Serédy-Andrássy (1663–1710?) entombed in Krásna Hôrka Castle, Slovakia 斯洛伐克Krásna Hôrka城堡出土的男爵夫人Zsófia Serédy-Andrássy（1663-1710 ?）木乃伊之谜解开

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

International Biodeterioration & Biodegradation

Pub Date : 2025-12-04 DOI: 10.1016/j.ibiod.2025.106256

Monika Huraiová , Stanislava Milovská , Adrián Biroň , Rastislav Milovský , Vratislav Hurai , Hana Vojtková , Michaela Dörnhöferová , Silvia Bodoriková

Microbiological investigations of skin, hair, and intra-corporeal tissue of the mummified body of Zsófia Serédy-Andrássy, who had been laid to rest in a glass coffin in the Krásna Hôrka Castle in southeastern Slovakia, revealed necrobiome dominated by the phylum Firmicutes followed by representatives of the phyla Actinobacteria and Proteobacteria. Optically visible bright-to-yellow mineral precipitates on the skin and organs are dominated by potassium sulphate (the mineral arcanite), with a minor admixture of chlorides (probably halite). Only a very rare calcium carbonate has been identified on the hair surface. The high concentrations of potassium in both tissue and hair, together with the ³⁴S-rich isotope compositions of keratin sulphur (δ³⁴S = 11.6–11.7‰ CDT) and skin leachate (δ³⁴S = 7.1–8.5‰ CDT), suggest either the excessive use of K₂SO₄ during medical treatment or intentional embalming – the first such documented case in Europe for the period. Biogenic microbial or fungal origin of essentially pure K₂SO₄ is highly unlikely. The high residual levels of non-excreted salts, combined with the dry microclimatic environment of church crypt, resulted in the body mummification and crystallization of potassium sulphate on the skin surface and internal organs. The commonly accepted conjecture regarding the natural mummification of Zsófia's corpse, which is believed to be caused by calcium hydrogen carbonate or calcium bicarbonate-rich drip water and subsequent desiccation, should be rejected.

在斯洛伐克东南部Krásna Hôrka城堡的玻璃棺材中，对木乃伊Zsófia Serédy-Andrássy的皮肤、头发和体内组织进行了微生物学调查，发现坏死菌群以厚壁菌门为主，其次是放线菌门和变形菌门的代表。皮肤和器官上可见光可见的亮至黄色矿物沉淀主要由硫酸钾（矿物隐石）和少量氯化物（可能是盐岩）组成。在毛发表面只发现了一种非常罕见的碳酸钙。组织和头发中的高浓度钾，以及角蛋白硫（δ34S = 11.6-11.7‰CDT）和皮肤渗出液（δ34S = 7.1-8.5‰CDT）的富34s同位素组成表明，要么是在医疗过程中过量使用K2SO4，要么是故意防腐——这是该时期欧洲第一个有记录的此类案例。纯K2SO4的生物源微生物或真菌来源是极不可能的。高残留的非排泄盐，加上教堂地窖干燥的小气候环境，导致尸体木乃伊化，皮肤表面和内脏器官的硫酸钾结晶。普遍接受的关于Zsófia尸体自然木乃伊化的猜想，被认为是由碳酸氢钙或富含碳酸氢钙的滴水和随后的干燥引起的，应该被拒绝。

{"title":"Resolving the mummification enigma of Baroness Zsófia Serédy-Andrássy (1663–1710?) entombed in Krásna Hôrka Castle, Slovakia","authors":"Monika Huraiová , Stanislava Milovská , Adrián Biroň , Rastislav Milovský , Vratislav Hurai , Hana Vojtková , Michaela Dörnhöferová , Silvia Bodoriková","doi":"10.1016/j.ibiod.2025.106256","DOIUrl":"10.1016/j.ibiod.2025.106256","url":null,"abstract":"<div><div>Microbiological investigations of skin, hair, and intra-corporeal tissue of the mummified body of Zsófia Serédy-Andrássy, who had been laid to rest in a glass coffin in the Krásna Hôrka Castle in southeastern Slovakia, revealed necrobiome dominated by the phylum <em>Firmicutes</em> followed by representatives of the phyla <em>Actinobacteria</em> and <em>Proteobacteria</em>. Optically visible bright-to-yellow mineral precipitates on the skin and organs are dominated by potassium sulphate (the mineral arcanite), with a minor admixture of chlorides (probably halite). Only a very rare calcium carbonate has been identified on the hair surface. The high concentrations of potassium in both tissue and hair, together with the <sup>34</sup>S-rich isotope compositions of keratin sulphur (δ<sup>34</sup>S = 11.6–11.7‰ CDT) and skin leachate (δ<sup>34</sup>S = 7.1–8.5‰ CDT), suggest either the excessive use of K<sub>2</sub>SO<sub>4</sub> during medical treatment or intentional embalming – the first such documented case in Europe for the period. Biogenic microbial or fungal origin of essentially pure K<sub>2</sub>SO<sub>4</sub> is highly unlikely. The high residual levels of non-excreted salts, combined with the dry microclimatic environment of church crypt, resulted in the body mummification and crystallization of potassium sulphate on the skin surface and internal organs. The commonly accepted conjecture regarding the natural mummification of Zsófia's corpse, which is believed to be caused by calcium hydrogen carbonate or calcium bicarbonate-rich drip water and subsequent desiccation, should be rejected.</div></div>","PeriodicalId":13643,"journal":{"name":"International Biodeterioration & Biodegradation","volume":"208 ","pages":"Article 106256"},"PeriodicalIF":4.1,"publicationDate":"2025-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145692439","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-resolved metagenomics of a neotropical wastewater treatment plant reveals community-wide metal and biocide-resistance genes and the diversity of phosphate-accumulating and denitrifying bacteria 新热带污水处理厂的基因组解析宏基因组学揭示了整个社区的金属和杀菌剂抗性基因以及磷酸盐积累和反硝化细菌的多样性

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

International Biodeterioration & Biodegradation

Pub Date : 2025-12-04 DOI: 10.1016/j.ibiod.2025.106258

Bradd Mendoza-Guido , Valeria Castro-Camacho , Andrea Quesada-Gonzalez , Luz Chacón , Mary Luz Barrios-Hernandez

Wastewater treatment plants (WWTPs) rely on complex microbial communities to remove nutrients and contaminants, yet tropical systems remain poorly characterized. This study applied genome-resolved metagenomics to investigate the taxonomic composition, functional potential, and adaptive traits of activated sludge from a domestic neotropical WWTP. From six sludge samples sampled across two different seasons in Costa Rica (rainy and dry), we reconstructed 177 non-redundant metagenome-assembled genomes (MAGs), of which 62 % were high-quality (90 % completeness and less 5 % contamination). Biocide and metal resistance genes (BMRGs) were widespread, particularly in Actinomycetia and Gammaproteobacteria, reflecting adaptation to selective environmental pressures. We identified 64 potential phosphate-accumulating organisms (PAOs), 78 denitrifying bacteria (DBs), and 32 denitrifying PAOs (DPAOs), with some MAGs showing negative correlations with effluent nitrogen and phosphorus concentrations, indicating roles in nutrient removal. While complete denitrification pathways were observed, nitrification genes were only partially recovered, underscoring both the limitations of metagenome-assembled genomes and the underrepresentation of some genetic variants in databases. Additionally, a high-quality MAG affiliated with Candidatus (Ca.) Accumulibacter clade IIF exhibited genomic divergence from known species, suggesting the presence of a potential novel lineage of this relevant genus. These findings demonstrate that tropical activated sludge harbors both well-known and novel taxa with key metabolic capacities, along with diverse adaptive traits to environmental stressors. Collectively, this study expands current knowledge of microbial diversity and functional potential in tropical WWTPs and provides a framework for future research aimed at improving wastewater treatment in underexplored regions.

污水处理厂（WWTPs）依靠复杂的微生物群落来去除营养物质和污染物，但热带系统的特征仍然很差。本研究应用基因组解析宏基因组学研究了国内新热带污水处理厂活性污泥的分类组成、功能潜力和适应特性。从哥斯达黎加两个不同季节（雨季和旱季）采集的六个污泥样本中，我们重建了177个非冗余宏基因组组装基因组（MAGs），其中62%是高质量的（完整性90%，污染低于5%）。杀菌剂和金属抗性基因（BMRGs）广泛存在，特别是在放线菌和γ变形菌中，反映了对选择性环境压力的适应。我们鉴定出64种潜在的磷酸盐积累生物（PAOs）， 78种反硝化细菌（DBs）和32种反硝化PAOs (DPAOs)，其中一些MAGs与出水氮和磷浓度呈负相关，表明它们在去除营养物中起作用。虽然观察到完整的反硝化途径，但硝化基因仅部分恢复，这强调了宏基因组组装基因组的局限性以及数据库中某些遗传变异的代表性不足。此外，与Candidatus (Ca.) Accumulibacter分支IIF相关的高质量MAG显示出与已知物种的基因组差异，表明该相关属存在潜在的新谱系。这些发现表明，热带活性污泥中既有已知的，也有具有关键代谢能力的新分类群，以及对环境胁迫的多种适应特征。总的来说，这项研究扩展了目前对热带污水处理厂微生物多样性和功能潜力的了解，并为未来旨在改善未开发地区废水处理的研究提供了一个框架。

{"title":"Genome-resolved metagenomics of a neotropical wastewater treatment plant reveals community-wide metal and biocide-resistance genes and the diversity of phosphate-accumulating and denitrifying bacteria","authors":"Bradd Mendoza-Guido , Valeria Castro-Camacho , Andrea Quesada-Gonzalez , Luz Chacón , Mary Luz Barrios-Hernandez","doi":"10.1016/j.ibiod.2025.106258","DOIUrl":"10.1016/j.ibiod.2025.106258","url":null,"abstract":"<div><div>Wastewater treatment plants (WWTPs) rely on complex microbial communities to remove nutrients and contaminants, yet tropical systems remain poorly characterized. This study applied genome-resolved metagenomics to investigate the taxonomic composition, functional potential, and adaptive traits of activated sludge from a domestic neotropical WWTP. From six sludge samples sampled across two different seasons in Costa Rica (rainy and dry), we reconstructed 177 non-redundant metagenome-assembled genomes (MAGs), of which 62 % were high-quality (90 % completeness and less 5 % contamination). Biocide and metal resistance genes (BMRGs) were widespread, particularly in Actinomycetia and Gammaproteobacteria, reflecting adaptation to selective environmental pressures. We identified 64 potential phosphate-accumulating organisms (PAOs), 78 denitrifying bacteria (DBs), and 32 denitrifying PAOs (DPAOs), with some MAGs showing negative correlations with effluent nitrogen and phosphorus concentrations, indicating roles in nutrient removal. While complete denitrification pathways were observed, nitrification genes were only partially recovered, underscoring both the limitations of metagenome-assembled genomes and the underrepresentation of some genetic variants in databases. Additionally, a high-quality MAG affiliated with Candidatus (Ca.) <em>Accumulibacter</em> clade IIF exhibited genomic divergence from known species, suggesting the presence of a potential novel lineage of this relevant genus. These findings demonstrate that tropical activated sludge harbors both well-known and novel taxa with key metabolic capacities, along with diverse adaptive traits to environmental stressors. Collectively, this study expands current knowledge of microbial diversity and functional potential in tropical WWTPs and provides a framework for future research aimed at improving wastewater treatment in underexplored regions.</div></div>","PeriodicalId":13643,"journal":{"name":"International Biodeterioration & Biodegradation","volume":"208 ","pages":"Article 106258"},"PeriodicalIF":4.1,"publicationDate":"2025-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145692434","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