Xiong F, Zhao X, Wen D, Li Q. Effects of N-acyl-homoserine lactones-based quorum sensing on biofilm formation, sludge characteristics, and bacterial community during the start-up of bioaugmented reactors. The Science of the total environment [Internet]. 2020;735:139449. 访问链接Abstract
Bioaugmentation is an effective technology for treating wastewater containing recalcitrant organic pollutants. However, it is restricted by several technical problems, including the difficult colonization and survival of the inoculated bacteria, and the time-consuming start-up process. Considering the important roles of quorum sensing (QS) in regulating microbial behaviors, this study investigated the effects of N-acyl-homoserine lactones (AHLs)-based manipulation on the start-up of biofilm reactors bioaugmented with a pyridine-degrading strain Paracoccus sp. BW001. The results showed that, in the presence of two specific exogenous AHLs (C6-HSL and 3OC6-HSL), the biofilm formation process on carriers was significantly accelerated, producing thick and structured biofilms. The protein and polysaccharide contents of the extracellular polymeric substances (EPS) and soluble microbial products (SMP) in sludge were also elevated, possibly due to the increased abundance of several EPS-producing bacterial genera. Specifically, the stability and complexity of protein structures were improved. Besides the reactor running time, the AHL-manipulation was proved to be the main factor that drove the shift of bacterial community structures in the reactors. The addition of exogenous AHLs significantly increased the succession rate of bacterial communities and decreased the bacterial alpha diversity. Most importantly, the final proportions of the inoculated strain BW001 were elevated by nearly 100% in both sludge and biofilm communities via the AHL-manipulation. These findings strongly elucidated that AHL-based QS was deeply involved in biofilm formation, sludge characteristics, and microbial community construction in bioaugmented reactors, providing a promising start-up strategy for bioaugmentation technology.
Zhao Y, Chen W, Wen D. The effects of crude oil on microbial nitrogen cycling in coastal sediments. Environment International [Internet]. 2020;139:105724. 访问链接Abstract
Crude oil could affect certain critical microbial processes of nitrogen cycling (N-cycling) in coastal sediments, and disturb the nitrogen balance. However, the understanding of the effects of crude oil on coastal sediments N-cycling under human disturbance was still limited. In this study, two sediments (named SY and HB with heavy and slight pollution, respectively) were sampled from Hangzhou Bay, China. After an incubation with exposure to different amounts of crude oil in above two sediments for 30 days, we found that crude oil affected microbial N-cycling in multiple levels. Potential rate measurements revealed that crude oil stimulated potential denitrification and N2O emissions in both sediments, which showed a higher influence on denitrification rates in higher concentration of oil. Quantitative PCR revealed that crude oil greatly increased abundances of bacterial and archaeal 16S rRNA genes and N-cycling genes (nirS, nosZ, nrfA, part of AOA and AOB amoA). On the other hand, only a few genes (16S rRNA and nrfA) showed higher transcriptional activities in oil-addition treatments. Results about relative changes of N-cycling genes revealed that the variations of N-cycling genes in oil-addition treatments were related to sediment types but not crude oil concentrations, and the genes in HB were more sensitive to crude oil than SY. Network analysis of N-cycling genes found that crude oil decreased the complexity of N-cycling gene networks in SY, while increased complexity in HB, and led to more competition among N-cycling microbes. Our findings help to look into the effects of crude oil on key N-cycling processes, and improve the understanding of the interactions among N-cycling under crude oil contamination.
Feifei L, Lyujun C, Weidong C, Yingyu B, Yuhan Z, Bei H, Qinglin M, Donghui W, Chuanping F. Antibiotics in coastal water and sediments of the East China Sea: Distribution, ecological risk assessment and indicators screening. Marine Pollution Bulletin [Internet]. 2020;151:110810. 访问链接
Tianjiao D, Yanan Z, Daliang N, Bei H, Qinglin M, Yunfeng Y, Donghui W. Dynamics of coastal bacterial community average ribosomal RNA operon copy number reflect its response and sensitivity to ammonium and phosphate. Environmental Pollution [Internet]. 2020:113971. 访问链接
Zhiguo S, Aolin L, Jiayu C, Bei H, Qinglin M, Lyujun C, Donghui W. Wastewater discharge drives ARGs spread in the coastal area: A case study in Hangzhou Bay, China. Marine Pollution Bulletin [Internet]. 2020;151:110856. 访问链接
熊富忠, 赵小希, 温东辉, 李琪琳. 一株吡啶降解菌Pseudomonas sp. ZX08的生物膜形成特性及影响因素. 微生物学通报 [Internet]. 2019. 访问链接AbstractPKU 
【背景】 煤化工企业排放的废水中含有大量难降解、高毒性的有机污染物,采用以高效降解菌为基础的生物强化技术对其进行处理,是一种经济可行的策略;而促进高效降解菌在载体材料表面的生物膜形成,有助于提升生物膜法废水处理系统的效能。【目的】 探究一株吡啶高效降解菌 Pseudomonas sp.ZX08 的生物膜形成过程和特性,识别不同的环境因子如温度、 pH、 Na+、 K+、Ca2+、 Mg2+等对其生物膜形成的影响规律,为实现人工调控其在实际废水处理系统中的成膜过程提供理论依据。【方法】 采用改良的微孔板生物膜培养与定量方法,以单因子影响实验测定不同条件下菌株在 12 孔板内的生物膜形成量和浮游态细菌量;采用激光共聚焦显微镜(confocal laser scanning microscope,CLSM)观察和分析生物膜的结构特征。【结果】 Pseudomonas sp. ZX08 菌株具有良好的吡啶降解性能,且生物膜形成能力较强, CLSM 观察到其在载体表面形成的生物膜可达到 40-50 mm;生物膜外层的活细胞比例更高,分泌的胞外蛋白也更多。 ZX08 菌株的生物膜形成量具有明显的周期性变化特征, 12 h、48 h 的生物膜量是相对峰值。 ZX08 生物膜形成的最适温度是 25 °C,最适 pH范围是 7.0-9.0;较高浓度的 NaCl (>0.6 mol/L)和 KCl (>0.4 mol/L)均对 ZX08的生物膜形成有显著的抑制作用;一定范围内(0-16 mmol/L) Ca2+浓度的提高可以促进 ZX08 在 12 孔板底部固-液界面生物膜的形成,浓度更高时则显著抑制生物膜的形成;一定范围内(0-16 mmol/L) Mg2+浓度的提高对 ZX08 生物膜形成有促进作用,但促进幅度不大。【结论】 吡啶降解菌 Pseudomonas sp. ZX08 的生物膜形成能力较强,未来在实际废水处理系统中应用时需要综合考虑各种环境因子对其生物膜形成的影响。
赵小希, 熊富忠, 温东辉, 李琪琳. 多株吡啶高效降解菌的降解性能与生物膜形成特性的研究. 北京大学学报 [Internet]. 2019;55(06):1129-1140. 访问链接AbstractPKU 
以吡啶为目标污染物,考察从焦化废水处理系统中分离的12株高效吡啶降解菌对吡啶的降解性能和生物膜形成特性,以期为在废水处理系统中构建降解型生物膜提供理论参考。结果表明:12株菌都具有较高的吡啶降解活性,其中代表性菌株Pseudomonas sp.ZX01和Arthrobacter sp.ZX07降解吡啶的最适温度是35°C,最适pH是7.0,在初始吡啶浓度为100~2000 mg/L的范围内,降解率均达到100%。不同菌株的生物膜形成能力差异明显,胞外蛋白分泌量、胞外多糖分泌量和由鞭毛参与的游动能力与各株菌的生物膜形成能力之间存在显著的正相关关系。 
Zheng Y, Su Z, Dai T, Li F, Huang B, Mu Q, Feng C, Wen D. Identifying human-induced influence on microbial community: A comparative study in the effluent-receiving areas in Hangzhou Bay. Frontiers of Environmental Science & Engineering [Internet]. 2019;13(9). 访问链接Abstract
Microbial community structure is affected by both natural processes and human activities. In coastal area, anthropegenetic activity can usually lead to the discharge of the effluent from wastewater treatment plant (WWTP) to sea, and thus the water quality chronically turns worse and marine ecosystem becomes unhealthy. Microorganisms play key roles in pollutants degradation and ecological restoration; however, there are few studies about how the WWTP effluent disposal influences coastal microbial communities. In this study, sediment samples were collected from two WWTP effluent-receiving areas (abbreviated as JX and SY) in Hangzhou Bay. First, based on the high-throughput sequencing of 16S rRNA gene, microbial community structure was analyzed. Secondly, several statistical analyses were conducted to reveal the microbial community characteristics in response to the effluent disposal. Using PCoA, the significant difference of in microbial community structure was determined between JX and SY; using RDA, water COD and temperature, and sediment available phosphate and ammonia nitrogen were identified as the key environmental factors for the community difference; using LDA effect size analysis, the most distinctive microbes were found and their correlations with environmental factors were investigated; and according to detrended beta-nearest-taxon-index, the sediment microbial communities were found to follow “niche theory”. An interesting and important finding was that in SY that received more and toxic COD, many distinctive microbes were related to the groups that were capable of degrading toxic organic pollutants. This study provides a clear illustration of eco-environmental deterioration under the long-term human pressure from the view of microbial ecology.
Tang Y, Dai T, Su Z, Hasegawa K, Tian J, Chen L, Wen D. A Tripartite Microbial-Environment Network Indicates How Crucial Microbes Influence the Microbial Community Ecology. Microbial Ecology [Internet]. 2019. 访问链接Abstract
Current technologies could identify the abundance and functions of specific microbes, and evaluate their individual effects on microbial ecology. However, these microbes interact with each other, as well as environmental factors, in the form of complex network. Determination of their combined ecological influences remains a challenge. In this study, we developed a tripartite microbial-environment network (TMEN) analysis method that integrates microbial abundance, metabolic function, and environmental data as a tripartite network to investigate the combined ecological effects of microbes. Applying TMEN to analyzing the microbial-environment community structure in the sediments of Hangzhou Bay, one of the most seriously polluted coastal areas in China, we found that microbes were well-organized into 4 bacterial communities and 9 archaeal communities. The total organic carbon, sulfate, chemical oxygen demand, salinity, and nitrogen-related indexes were detected as crucial environmental factors in the microbial-environmental network. With close interactions with these environmental factors, Nitrospirales and Methanimicrococcu were identified as hub microbes with connection advantage. Our TMEN method could close the gap between lack of efficient statistical and computational approaches and the booming of large-scale microbial genomic and environmental data. Based on TMEN, we discovered a potential microbial ecological mechanism that crucial species with significant influence on the microbial community ecology would possess one or two of the community advantages for enhancing their ecological status and essentiality, including abundance advantage and connection advantage.
Chen J, Su Z, Dai T, Huang B, Mu Q, Zhang Y, Wen D. Occurrence and distribution of antibiotic resistance genes in the sediments of the East China Sea bays. Journal of Environmental Sciences [Internet]. 2019;81:156-167. 访问链接Abstract
The coastal area of the East China Sea has experienced rapid urbanization and industrialization in China since 1980s, resulting in severe pollution of its environments. Antibiotic resistance genes (ARGs) are regarded as a kind of emerging pollutant with potential high risk. The sediment samples were collected from Hangzhou Bay (HB), Xiangshan Bay (XB), and Taizhou Bay (TB) to investigate the spatial occurrence and distribution of 27 ARGs and class I integron–integrase gene (intI1) in the coastal area of the East China Sea. The PCR results showed the frequent presence of 11 ARGs and intI1 in the sediments of the three bays. The qPCR results further showed that sulfonamide resistance was the most prevalent ARG type and antibiotic target replacement and protection were the most important resistance mechanisms in the sediments. Regarding the subtype of ARGs, sulI, tetW, and dfrA13 were the most abundant ARGs, in which sulI was higher in TB (based on both the absolute and relative abundances) and dfrA13 was higher in HB (based on the relative abundances). The network analysis revealed that intI1 had significant correlations with tetC, sulI, sulII, and blaPSE-1. Oil was the key connected factor, which had positive connections with sulI, sulII, and blaPSE-1. In addition, the joint effect of heavy metals and nutrients & organic pollutants might be crucial for the fate of ARGs in the coastal sediments.
Dai T, Zhang Y, Ning D, Su Z, Tang Y, Huang B, Mu Q, Wen D. Dynamics of Sediment Microbial Functional Capacity and Community Interaction Networks in an Urbanized Coastal Estuary. Frontiers in Microbiology [Internet]. 2018. 访问链接Abstract
Coastal estuaries and bays are exposed to both natural and anthropogenic environmental changes, inflicting intensive stress on the microbial communities inhabiting these areas. However, it remains unclear how microbial community diversity and their eco-functions are affected by anthropogenic disturbances rather than natural environmental changes. Here, we explored sediment microbial functional genes dynamics and community interaction networks in Hangzhou Bay (HZB), one of the most severely polluted bays on China’s eastern coast. The results indicated key microbial functional gene categories, including N, P, S, and aromatic compound metabolism, and stress response, displayed significant spatial dynamics along environmental gradients. Sensitive feedbacks of key functional gene categories to N and P pollutants demonstrated potential impacts of human-induced seawater pollutants to microbial functional capacity. Seawater ammonia and dissolved inorganic nitrogen (DIN) was identified as primary drivers in selecting adaptive populations and varying community composition. Network analysis revealed distinct modules that were stimulated in inner or outer bay. Importantly, the network keystone species, which played a fundamental role in community interactions, were strongly affected by N-pollutants. Our results provide a systematic understanding of the microbial compositional and functional dynamics in an urbanized coastal estuary, and highlighted the impact of human activities on these communities.
Li A, Chen L, Zhang Y, Tao Y, Xie H, Li S, Sun W, Pan J, He Z, Mai C, et al. Occurrence and distribution of antibiotic resistance genes in the sediments of drinking water sources, urban rivers, and coastal areas in Zhuhai, China. Environmental Science and Pollution Research [Internet]. 2018;25(26):26209-26217. 访问链接Abstract
Antibiotic resistance genes (ARGs) are regarded as emerging contaminants related with human activities. Aquatic environments of an urban city are apt for the persistence and prevalence of ARGs. In this study, we investigated the occurrence and distribution of ARGs and integrase genes in the sediment samples collected from drinking water sources, urban rivers, and coastal areas of Zhuhai, China, in the dry and wet seasons of 2016. The results show that sulfonamide resistance gene of sulII was present at the highest detection frequency (85.71%); and its average concentrations were also the highest in both dry and wet seasons (3.78×107 and 9.04×107 copies/g sediment, respectively), followed by tetC, tetO, tetA, ermB, dfrA1, and blaPSE-1. Temporally, the concentrations of total ARGs in the wet season were likely higher than those in the dry season; and spatially, the concentrations of total ARGs in the drinking water sources were substantially lower than those in the urban rivers and nearby coastal areas, indicating the different degrees of anthropogenic impact and consequent health risks. Positive correlations were found between intI1 and each quantitative ARG in all wet season samples rather than dry season samples, which suggested higher temperature and more rain in summer might have positive influences on ARG dissemination, especially that mediated by intI1 gene and class I integrons.
Su Z, Dai T, Tang Y, Tao Y, Huang B, Mu Q, Wen D. Sediment bacterial community structures and their predicted functions implied the impacts from natural processes and anthropogenic activities in coastal area. Marine Pollution Bulletin [Internet]. 2018;131:481-495. 访问链接Abstract
Coastal ecosystem structures and functions are changing under natural and anthropogenic influences. In this study, surface sediment samples were collected from disturbed zone (DZ), near estuary zone (NEZ), and far estuary zone (FEZ) of Hangzhou Bay, one of the most seriously polluted bays in China. The bacterial community structures and predicted functions varied significantly in different zones. Firmicutes were found most abundantly in DZ, highlighting the impacts of anthropogenic activities. Sediment total phosphorus was most influential on the bacterial community structures. Predicted by PICRUSt analysis, DZ significantly exceeded FEZ and NEZ in the subcategory of Xenobiotics Biodegradation and Metabolism; and DZ enriched all the nitrate reduction related genes, except nrfA gene. Seawater salinity and inorganic nitrogen, respectively as the representative natural and anthropogenic factor, performed exact-oppositely in nitrogen metabolism functions. The changes of bacterial community compositions and predicted functions provide a new insight into human-induced pollution impacts on coastal ecosystem.
李奥林, 陈吕军, 张衍, 代天娇, 田金平, 刘锐, 温东辉. 抗生素抗性基因在两级废水处理系统中的分布和去除. 环境科学 [Internet]. 2018;39(10):4593-4600. 访问链接AbstractPKU 
熊富忠, 赵小希, 廖胤皓, 温东辉, 李琪琳. 材料表面特征对生物膜形成的影响及其应用. 微生物学通报 [Internet]. 2018;45(1):155-165. 访问链接AbstractPKU 
苏志国, 张衍, 代天娇, 陈嘉瑜, 张永明, 温东辉. 环境中抗生素抗性基因与I型整合子的研究进展. 微生物学通报 [Internet]. 2018;45(10):2217~2233. 访问链接AbstractPKU 
 抗生素抗性基因(Antibiotic resistance genes,ARGs)作为一种新型污染物在不同环境中广泛分布、来源复杂,对生态环境和人类健康造成了很大的潜在风险。同时,I型整合子(Int I)介导的ARGs水平转移是环境中微生物产生耐药性的重要途径,I型整合子整合酶基因(intI1)与ARGs丰度在环境中表现出了较高的正相关性,Int I可以作为标记物在一定程度上反映ARGs在环境中的迁移转化规律和人类活动影响程度。本文介绍ARGs与Int I在环境中的来源与分布,总结Int I介导的ARGs迁移转化机制以及相关研究方法,并展望未来的研究发展趋势。
何静林, 温东辉, 高波. 杭州萧山区饮用水源地铁污染评价及控制对策研究. 中国环境监测 [Internet]. 2017;33(1):97-105. 访问链接AbstractPKU 
Zhang Y, Li A, Dai T, Li F, Xie H, Chen L, Wen D. Cell-free DNA: a neglected source for antibiotic resistance genes spreading from WWTPs. Environmental Science & Technology [Internet]. 2017;52(1):248-257. 访问链接Abstract
Cell-associated ARGs in wastewater treatment plants (WWTPs) has been concerned, however, cell-free ARGs in WWTPs was rarely studied. In this study, the abundances of four representative ARGs, sulII, tetC, blaPSE‑1,and ermB, in a large municipal WWTP were investigated in both cell-associated and cell-free fractions. Cell-associated ARGs was the dominant ARGs fraction in the raw wastewater. After biological treatment, sludge settling, membrane filtration, and disinfection, cell-associated ARGs were substantially reduced, though the ratios of ARG/16S rRNA gene were increased with disinfection. Cell-free ARGs persisted in the WWTP with a removal of 0.36 log to 2.68 logs, which was much lower than the removal of cell-associated ARGs (3.21 logs to 4.14 logs). Therefore, the abundance ratio of cell-free ARGs to cell-associated ARGs increased from 0.04−1.59% to 2.00−1895.08% along the treatment processes. After 25-day-storage, cell-free ARGs in both biological effluent and disinfection effluent increased by 0.14 log to 1.99 logs and 0.12 log to 1.77 logs respectively, reflecting the persistence and low decay rate of cell-free ARGs in the discharge water. Therefore, cell-free ARGs might be a kind of important but previously neglected pollutant from WWTPs, which added potential risks to the effluent receiving environments.
张衍, 陈吕军, 谢辉, 李奥林, 代天娇. 两座污水处理系统中细胞态和游离态抗生素抗性基因的丰度特征. 环境科学 [Internet]. 2017;38(9):3823-3830. 访问链接AbstractPKU 
为探究污水处理系统中抗生素抗性基因(ARGs)、特别是胞外游离态ARGs的赋存特征,本研究选取生活污水处理系统和工业废水处理系统各一座,采用荧光定量PCR对细胞态及游离态ARGs丰度变化开展研究.在生活污水处理系统M中,进水sulⅡ、tet C、bla PSE-1erm B这4种ARGs细胞态的绝对丰度均大幅高于游离态的绝对丰度,生物处理未对抗生素抗性菌(ARBs)产生富集效应;MBR的超滤膜有效削减了水中细胞态和游离态DNA,最终ARGs的总去除率为2.54~4.95 logs.在焦化废水处理系统C中,生物处理对携带sulⅡ的ARBs产生了富集效应,但游离态sulⅡ的相对丰度和绝对丰度均有所降低;其后混凝-砂滤工艺使水中细胞态和游离态sulⅡ的绝对丰度分别出现了下降和上升,游离态sulⅡ在总sulⅡ中的比例从生物处理出水中的0.05%,上升到混凝-砂滤出水中的1.33%,并在25℃恒温避光静置5d后进一步上升至9.31%.ARBs深度去除及残留细胞裂解,使污水处理系统出水中游离ARGs在总ARGs中的比例有所上升.游离态ARGs介导ARGs在污水处理系统出水受纳环境中的传播扩散风险有待后续研究进行深入评估.
陶怡乐, 张晨枫, 徐琳, 温东辉. 北京大学未名湖水质与底泥菌群结构的时空变化. 北京大学学报(自然科学版) [Internet]. 2017;53(6):1150-1160. 访问链接Abstract