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
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
方元狄, 张静, 郑中原, 温东辉. 焦化废水处理试验系统出水的生物毒性变化. 生态毒理学报 [Internet]. 2017;12(3):317-326. 访问链接AbstractPKU 
焦化废水是一种典型的难降解工业废水,组分复杂,生物毒性高,大多采用生物处理联合物化深度处理的工艺,以满足炼焦化学工业的污染排放标准,但其排水安全性仍然令人担忧。为研究工艺排水安全性,选择发光细菌青海弧菌Q67、稀有鮈鲫(Gobiocypris rasus)血红细胞、活性污泥微生物群落为测试生物,研究了焦化废水及各处理阶段出水的急性毒性和遗传毒性变化,进而识别影响生物毒性的水质因子。焦化废水经过序批式生物膜反应器处理后,出水急性毒性比进水下降71%,遗传毒性下降为90%以上的轻度以下损伤,显示生物强化处理对焦化废水生物毒性有良好的去除作用。生物处理出水再经过深度处理后,则表现出不同的毒性变化:活性炭吸附法对生物急性毒性的消除最佳,但遗传毒性较生物处理出水有所升高;臭氧氧化法不仅水质改善效率差,且最终出水的生物急性毒性与遗传毒性均升高;臭氧催化氧化法对水中残留有机物去除效率较高,但也造成出水急性毒性与遗传毒性的升高。各水样对青海弧菌Q67的急性毒性与有机物、氮等水质指标表现出较强相关性,而遗传毒性与水质指标之间的相关性不显著。研究结果可为评价和改进处理工艺、保障水体生态安全提供参考。
Dai T, Zhang Y, Tang Y, Bai Y, Tao Y, Huang B, Wen D. Identifying the key taxonomic categories that characterize microbial community diversity using full-scale classification: a case study of microbial communities in the sediments of Hangzhou Bay. FEMS Microbiology Ecology [Internet]. 2016;92(10):fiw150. 访问链接Abstract
Coastal areas are land–sea transitional zones with complex natural and anthropogenic disturbances. Microorganisms in coastal sediments adapt to such disturbances both individually and as a community. The microbial community structure changes spatially and temporally under environmental stress. In this study, we investigated the microbial community structure in the sediments of Hangzhou Bay, a seriously polluted bay in China. In order to identify the roles and contribution of all microbial taxa, we set thresholds as 0.1% for rare taxa and 1% for abundant taxa, and classified all operational taxonomic units into six exclusive categories based on their abundance. The results showed that the key taxa in differentiating the communities are abundant taxa (AT), conditionally abundant taxa (CAT), and conditionally rare or abundant taxa (CRAT). A large population in conditionally rare taxa (CRT) made this category collectively significant in differentiating the communities. Both bacteria and archaea demonstrated a distance decay pattern of community similarity in the bay, and this pattern was strengthened by rare taxa, CRT and CRAT, but weakened by AT and CAT. This implied that the low abundance taxa were more deterministically distributed, while the high abundance taxa were more ubiquitously distributed.
Yu C, Li X, Zhang N, Wen D, Liu C, Li Q. Inhibition of biofilm formation by D-tyrosine: Effect of bacterial type and D-tyrosine concentration. Water research [Internet]. 2016;92:173-9. 访问链接Abstract
D-Tyrosine inhibits formation and triggers disassembly of bacterial biofilm and has been proposed for biofouling control applications. This study probes the impact of D-tyrosine in different biofilm formation stages in both G+ and G- bacteria, and reveals a non-monotonic correlation between D-tyrosine concentration and biofilm inhibition effect. In the attachment stage, cell adhesion was studied in a flow chamber, where D-tyrosine caused significant reduction in cell attachment. Biofilms formed by Pseudomonas aeruginosa and Bacillus subtilis were characterized by confocal laser scanning microscopy as well as quantitative analysis of cellular biomass and extracellular polymeric substances. D-Tyrosine exhibited strong inhibitive effects on both biofilms with  an effective concentration as low as 5 nM; the biofilms responded to D-tyrosine concentration change in a non-monotonic, bi-modal pattern. In addition, D-tyrosine showed notable and different impact on EPS production by G+ and G- bacteria. Extracellular protein was decreased in P. aeruginosa biofilms, but increased in those of B. subtilis. Exopolysaccharides production by P. aeruginosa was increased at low concentrations and reduced at high concentrations while no impact was found in B. subtilis. These results suggest that distinct mechanisms are at play at different D-tyrosine concentrations and they may be species specific. Dosage of D-tyrosine must be carefully controlled for biofouling control applications.
Zhang Y, Chen L, Sun R, Dai T, Tian J, Zheng W, Wen D. Population and diversity of ammonia-oxidizing archaea and bacteria in a pollutants’ receiving area in Hangzhou Bay. Applied Microbiology and Biotechnology [Internet]. 2016;100(13):6035-6045. 访问链接Abstract
The community structure of ammonia-oxidizing microorganisms is sensitive to various environmental factors, including pollutions. In this study, real-time PCR and 454 pyrosequencing were adopted to investigate the population and diversity of ammonia-oxidizing archaea (AOA) and bacteria (AOB) temporally and spatially in the sediments of an industrial effluent receiving area in the Qiantang River’s estuary, Hangzhou Bay. The abundances of AOA and AOB amoA genes fluctuated in 105–107 gene copies per gram of sediment; the ratio of AOA amoA/AOB amoA ranged in 0.39–5.52. The AOA amoA/archaeal 16S rRNA, AOB amoA/bacterial 16S rRNA, and AOA amoA/AOB amoA were found to positively correlate with NH4+-N concentration of the seawater. Nitrosopumilus cluster and Nitrosomonas-like cluster were the dominant AOA and AOB, respectively. The community structures of both AOA and AOB in the sediments exhibited significant seasonal differences rather than spatial changes in the effluent receiving area. The phylogenetic distribution of AOB in this area was consistent with the wastewater treatment plants (WWTPs) discharging the effluent but differed from the Qiantang River and other estuaries, which might be an outcome of long-term effluent discharge.
Zhang Y, Chen L, Sun R, Dai T, Tian J, Zheng W, Wen D. Temporal and spatial changes of microbial community in an industrial effluent receiving area in Hangzhou Bay. Journal of Environmental Sciences [Internet]. 2016;44:57-68. 访问链接Abstract
Anthropogenic activities usually contaminate water environments, and have led to the eutrophication of many estuaries and shifts in microbial communities. In this study, the temporal and spatial changes of the microbial community in an industrial effluent receiving area in Hangzhou Bay were investigated by 454 pyrosequencing. The bacterial community showed higher richness and biodiversity than the archaeal community in all sediments. Proteobacteria dominated in the bacterial communities of all the samples; Marine_Group_I and Methanomicrobia were the two dominant archaeal classes in the effluent receiving area. PCoA and ANOVA revealed strong seasonal but minor spatial changes in both bacterial and archaeal communities in the sediments. The seasonal changes of the bacterial community were less significant than those of the archaeal community, which mainly consisted of fluctuations inabundance of a large proportion of longstanding species rather than the appearance and disappearance ofmajor archaeal species. Temperaturewas found to positively correlatewith the dominant bacteria, Betaproteobacteria, and negatively correlate with the dominant archaea,Marine_Group_I; and might be the primary driving force for the seasonal variation of the microbial community.
张楠, 熊富忠, 温东辉, 于聪, 李琪琳. 环境因素对降解型生物膜形成的影响. 北京大学学报(自然科学版) [Internet]. 2016;52(2):345-353. 访问链接Abstract
采用改良微孔板法,考察p H、温度、培养时间和目标污染物浓度4个环境因子对3株氮杂环芳烃降解菌成膜的影响。结果表明,p H、温度、培养时间对生物膜的形成影响显著,且各降解菌的最佳成膜条件分别为:BC026成膜的最适p H为7,最适温度为35℃,培养时间为36小时;BW001成膜的最适p H为8,最适温度为35℃,培养时间为48小时;BW004成膜的最适p H为7~9,最适温度为40℃,培养时间为36小时。在0~1600 mg/L的目标污染物浓度内,目标污染物对生物膜形成的影响不显著。
陶怡乐, 温东辉. 细菌硝酸盐异化还原成铵过程及其在河口生态系统中的潜在地位与影响. 微生物学通报 [Internet]. 2016;43(1):172-181. 访问链接AbstractPKU