基于病毒宏基因组学鉴定水环境中噬菌体携带的新型耐药基因及其耐药特点分析

水环境作为耐药基因的存储库，为耐药基因的水平转移和新型耐药基因的产生提供重要场所.但到目前为止，对水环境中病毒携带耐药基因的特征及其功能还知之甚少.因此以南四湖和东平湖为研究对象，利用病毒宏基因组学结合体外实验的方法探讨水环境中病毒携带新型耐药基因的情况及其耐药特点.通过分析病毒基因组的片段（reads）和重叠群（contigs），鉴定出多种耐药基因，包括AAC（6’）、Qnr A、Van Y、Vat和β-内酰胺酶基因.值得关注的是，通过核心序列比对和进化分析，挖掘出两种噬菌体携带的新型β-内酰胺酶基因bla_NSDPV-1和bla_NSVM-1.最小抑菌浓度试验表明，这两种编码新型β-内酰胺酶的耐药基因对临床常用头孢类和碳青霉烯类抗生素具有一定的耐药性.综上所述，水环境中噬菌体很可能在新型耐药基因的产生和耐药基因散播中起着重要的作用.另外，病毒宏基因组学结合体外实验是发现噬菌体携带新型耐药基因的重要方法.     

象山港海洋病毒时空分布特征及其环境影响因素

分别于2007年的7月(夏季)、11月(秋季)与2008年的1月(冬季)、4月(春季)采集样品,研究了象山港海域的水样(表层海水和上覆水)中的浮游病毒及沉积物中的底层病毒丰度的时空分布特征,并采用主成分分析及多元逐步回归分析方法研究了影响浮游病毒丰度时空分布的主要因素,结果表明,调查期间象山港海域表层海水、上覆水及沉积物样品中浮游(底层)病毒丰度实测值的变化范围为6.48×104~1.01×108cells/mL,均值分别为1.55×107,1.03×108,1.13×108cells/mL.季节分布特征为秋季 > 夏季 > 春季 > 冬季.病毒丰度垂直分布表现为上覆水均大于表层海水;平面分布均为从港底到港口递减、养殖区高于非养殖区、电厂附近海域出现较高值的趋势.近岸人类活动的陆源污染及水产养殖污染是造成此空间分布特征的主要原因.溶解氧、水温及叶绿素a是制约表层海水浮游病毒丰度的主要影响因素;营养盐含量及浮游细菌丰度是制约上覆水中浮游病毒丰度的主要影响因素,沉积物中的病毒丰度与细菌丰度具有显著正相关性(P < 0.01).     

一体化A2/O-MBR系统中抗性基因分布及去除效果研究

选取北京市某农村一体化A²/O-MBR污水处理系统,系统研究了系统中抗生素抗性基因（Antibiotic Resistance Genes,ARGs）及病原菌在全流程各个处理单元中的分布特征,基于宏基因组学的高通量测序技术对农村生活污水进水、MBR池中污泥和出水样品中ARGs及病原菌的丰度变化及去除效果进行了系统分析.结果表明：ARGs广泛存在于污水处理系统中,共检测出包括tetracycline类、aminoglycoside类和sulfonamide类在内的19类ARGs,进水中ARGs的相对丰度远远高于其在出水中的浓度,通过污水处理系统后ARGs相对丰度下降了72.25%,而大多数的ARGs在污水处理系统并不能得到完全去除.微生物群落结构变化显示,32种潜在病原体相对丰度下降明显,但大多数病原菌也无法得到完全去除.出水中残留的ARGs和病原菌仍会对受纳水体造成一定的潜在污染风险.     

1960年-2014年天山北麓气温和降水变化趋势及预测研究

利用天山北麓17个气象站点1960年-2014年的气温和降水资料,采用Morlet小波分析、R/S分析等,研究了天山北麓气温和降水的时间变化.结果表明,(1)天山北麓年平均气温和年降水量分别以0.035℃/a和0.881 mm/a的倾向率呈上升趋势;季节变化明显;(2)年平均气温和年降水量有明显的周期性,年平均气温在55 a尺度内存在13 a的强显著周期,年降水量在55 a尺度内存在8 a的强显著周期.(3)未来一段时间内,天山北麓气温和降水均呈上升趋势,且与过去的变化趋势持续性较强.     

微塑料对沉积物细菌群落组成和多样性的影响

微塑料普遍存在于河口、海岸和深海沉积物中,能直接或间接地对沉积环境中细菌和真菌群落产生影响.为探究微塑料对沉积物细菌群落组成和多样性的影响,通过向沉积物中分别添加不同丰度(2%、 5%、 10%)和类型(PE、 PVC)的微塑料颗粒,进行30 d的微塑料污染模拟实验,分析不同微塑料处理中微生物群落结构和多样性差异.结果表明,微塑料对菌群多样性无显著影响,但能降低群落丰富度,且添加PE和10%PVC下降最显著;添加微塑料使放线菌门、拟杆菌门和酸杆菌门等相对丰度上升,后壁菌门相对丰度显著下降;伯克霍尔德氏菌科和假单胞菌科等涉及氮循环的菌群在添加PE以及2%和10%PVC后相对丰度显著增加,而鞘氨醇单胞菌科等与多种有害污染物生物降解作用有关菌群的相对丰度明显下降;KEGG代谢通路预测显示,添加PE和较高丰度(5%、 10%)PVC使菌群膜转运蛋白、细胞运动和外源物质生物降解等功能显著改善,氨基酸代谢、碳水化合物代谢和能量代谢等功能受到抑制.研究可为微塑料污染对沉积物养分转化和外源污染物降解的影响研究提供理论基础.     

微塑料及金属在黄浦江地表水环境的赋存特征及与金属抗性基因的相关性分析

城市河流是微塑料(MPs)及重金属污染的“热点”区域,在污染迁移中起到重要作用.然而同样作为抗性基因赋存及释放的重要媒介,鲜有研究考察了流域MPs、金属与金属抗性基因(MRGs)的关联.为此,调研了10个黄浦江站点水样的金属及MPs的污染特征,并基于宏基因组学对水样及提取的MPs上的MRGs及可移动遗传元件(MGEs)进行分析.结果显示,表层水中ρ[锑(Sb)]平均值最高,为(3.16±0.419)μg·L^-1. MPs的丰度平均值为(1.78±0.84)n·L^-1,位于工业区和人口密集区的MPs丰度显著高于农业区和低人口密度的区域.纤维状、“小粒径”(<0.5 mm)的聚对苯二甲酸乙二醇酯(PET)是最主要的MPs类型.所有样本中共检出18类MRGs,其中水样中MRGs的相对丰度为1.68±0.21.最主要的MRGs亚型是merR和ruvB,分别为汞和多重金属抗性基因的亚型.相关性分析表明,水中的铬和镍与MRG-Cr、MRG-Ni和多重金属抗性基因之间存在显著正相关.MPs上MRGs的相对丰度为1.63±0.53,最主要的MRGs亚型...     

紫外氯胺组合消毒供水系统中病毒微生物的分布特征

为研究紫外氯胺组合消毒对供水系统中病毒微生物的影响特性,以生产规模紫外氯胺组合消毒供水系统为研究对象,应用宏基因组技术对供水系统中病毒微生物的迁移变化、群落结构和病毒宿主进行了分析.结果表明,紫外氯胺组合消毒工艺能降低病毒物种数（6.13%）和基因丰度（51.97%）,但不能完全去除水中病毒微生物.对比美国环保署（USEPA）以培养法检测的水处理病毒去除率可达99%~99.99%,本研究利用宏基因组技术测得的总病毒去除率只有93.46%,以培养法检测水中病毒存在局限性.Caudovirales（有尾噬菌体目）是整个供水系统中最丰富病毒,对氯胺消毒都具有一定敏感性.Lentivirus（慢病毒属）作为能够感染人和脊椎动物的病毒,对紫外照射和氯胺消毒都具有强抵抗力.该供水系统中最大的病毒宿主是细菌（61.50%）.原水中病毒主要寄生在Synechococcus（聚球藻属）中;出厂水以及管网水中,优势病毒宿主均为Pseudomonas（假单胞菌属）;进入管网后,Pseudomonas aeruginosa（铜绿假单胞菌）宿主病毒基因丰度升高342.62%,应加强关注管网系统病毒微生物风险.紫外氯胺组合消毒工艺比单紫外消毒更有利于病毒宿主的去除（51.97%与0.79%）.     

噬菌体编码的抗生素抗性基因研究进展

噬菌体作为地球上丰度最高的生物体,对于全球生态系统的微生物群落组成与动态,生物地球化学循环和细菌进化等都具有重要作用,但噬菌体对抗生素抗性的贡献还所知甚少.通过宏基因组测序和定量PCR等技术,发现了海洋,河流,土壤,动物肠道等环境的噬菌体基因组中存在多种耐药基因(antibiotic resistance genes,ARGs).因此,噬菌体及其介导的转导作用可能对ARGs的富集扩散发挥着重要作用.本文综述了不同环境介质的噬菌体基因组中ARGs的分布特征以及噬菌体介导的ARGs水平转移的研究进展,同时展望了为阐明噬菌体对抗生素抗性贡献需要解决的科学问题.本文将为了解噬菌体在ARGs传播扩散中的作用以及扩展对可移动抗性组的认知奠定基础.     

富营养化水体中浮游病毒与浮游植物生长的关系

于2005年4～12月对武汉东湖落雁岛和关桥2个池塘进行综合调查,考察浮游病毒丰度和叶绿素a含量的变化,以及水温、pH值、溶解氧量、总氮和总磷等环境因子的变化,分析浮游病毒与浮游植物、环境因子之间的相互关系.结果表明,在营养水平较高的水体中,浮游病毒丰度相应较高,但与营养物浓度变化无显著的相关性.2个采样点浮游病毒的平均丰度分别为2.99×10⁸,4.24×10⁸VLPs/mL(峰值出现在9、10月份).叶绿素a浓度的平均值分别为96.66,166.74μg/L.关桥采样点的浮游病毒丰度与前一个月的叶绿素a浓度呈显著相关(r=0.809,P<0.01),其显著性水平高于与当月叶绿素a浓度的相关性(r=0.634,P<0.05),而浮游病毒丰度与后一个月的叶绿素a浓度不呈显著相关(P>0.05).     

反硝化脱硫工艺中微生物群落结构及动态分析

为了研究反硝化脱硫工艺(denitrifying sulfide removal,DSR)中微生物群落与工艺运行的相关性,实验提取了反应器运行不同阶段污泥样品中微生物的全基因组DNA,利用高通量宏基因组学技术———基因芯片来解析各阶段功能微生物群落的结构特征及其演替过程.通过对功能基因的Simpson、Shannon多样性指数和聚类分析表明,微生物群落结构会随着反应器运行的阶段进行相应调整,且变化较大.在运行的前两个阶段,由于不适应环境,微生物群落的多样性指数比起始时明显减少,随着反应器的运行污泥逐渐成熟,多样性指数迅速增加,也标志着反应器进入稳定运行阶段.通过对反硝化脱硫过程中关键基因相对丰度的分析发现,功能基因的丰度不仅能反映功能菌群的活性,而且与工艺处理效果密切相关.     

Human viral pathogens are pervasive in wastewater treatment center aerosols

Wastewater treatment center(WTC) workers may be vulnerable to diseases caused by viruses, such as the common cold, influenza and gastro-intestinal infections. Although there is a substantial body of literature characterizing the microbial community found in wastewater, only a few studies have characterized the viral component of WTC aerosols,despite the fact that most diseases affecting WTC workers are of viral origin and that some of these viruses are transmitted through the air. In this study, we evaluated in four WTCs the presence of 11 viral pathogens of particular concern in this milieu and used a metagenomic approach to characterize the total viral community in the air of one of those WTCs. The presence of viruses in aerosols in different locations of individual WTCs was evaluated and the results obtained with four commonly used air samplers were compared.We detected four of the eleven viruses tested, including human adenovirus(h Ad V),rotavirus, hepatitis A virus(HAV) and Herpes Simplex virus type 1(HSV1). The results of the metagenomic assay uncovered very few viral RNA sequences in WTC aerosols, however sequences from human DNA viruses were in much greater relative abundance.     

Distribution and source of microplastics in China's second largest reservoir - Danjiangkou Reservoir

Fresh water microplastic pollution is of pressing concern globally, but its distribution and sources in reservoirs are poorly documented. Danjiangkou Reservoir is the second largest reservoir in China and is divided into the Han Reservoir and Dan Reservoir. In this work, microplastic abundances and morphological characteristics of the reservoir were investigated. The microplastic abundance of 15 main tributaries of the reservoir was also measured. The vertical distribution (in water column and sediment), horizontal distribution (in Han Reservoir and Dan Reservoir) and source of microplastics were analyzed. Microplastics accumulated in the middle layer of the reservoir, and the size and color of the microplastic particles changed from the surface to the bottom, which implies that surveys of surface water are not enough to determine the microplastic contamination for deep water reservoirs. In the surface water, the microplastic abundance in the Han Reservoir was lower than that in the Dan Reservoir (p < 0.05), but microplastic abundance did not differ significantly in the intermediate and bottom water. Tributaries were one of the main sources of microplastics for Han Reservoir but not for Dan Reservoir. Agricultural cultivation in the hydro-fluctuation belt might be an important source of microplastics in the Dan Reservoir, which should be given additional attention. The results of this study can provide valuable information for developing microplastic sampling strategies in deep water reservoirs. Further studies are recommended to investigate the process through which microplastics in the hydro-fluctuation belt enter the reservoir and the sinking behavior of microplastics in the reservoir.     

One-year Surveillance of Human Enteric Viruses in Raw and Treated Wastewaters,Downstream River Waters,and Drinking Waters

Human enteric viruses are a major cause of waterborne diseases, and can be transmitted by contaminated water of all kinds, including drinking and recreational water. The objectives of the present study were to assess the occurrence of enteric viruses (enterovirus, norovirus, adenovirus, hepatitis A and E virus) in raw and treated wastewaters, in rivers receiving wastewater discharges, and in drinking waters. Wastewater treatment plants’ (WWTP) pathogen removal efficiencies by adenovirus quantitative real-time PCR and the presence of infectious enterovirus, by cell culture assays, in treated wastewaters and in surface waters were also evaluated. A total of 90 water samples were collected: raw and treated wastewaters (treated effluents and ultrafiltered water reused for industrial purposes), water from two rivers receiving treated discharges, and drinking water. Nested PCR assays were used for the identification of viral DNA/RNA, followed by direct amplicon sequencing. All raw sewage samples (21/21), 61.9 % of treated wastewater samples (13/21), and 25 % of ultrafiltered water samples (3/12) were contaminated with at least one viral family. Multiple virus families and genera were frequently detected. Mean positive PCRs per sample decreased significantly from raw to treated sewage and to ultrafiltered waters. Moreover, quantitative adenovirus data showed a reduction in excess of 99 % in viral genome copies following wastewater treatment. In surface waters, 78.6 % (22/28) of samples tested positive for one or more viruses by molecular methods, but enterovirus-specific infectivity assays did not reveal infectious particles in these samples. All drinking water samples tested negative for all viruses, demonstrating the effectiveness of treatment in removing viral pathogens from drinking water. Integrated strategies to manage water from all sources are crucial to ensure water quality.     

Comprehensive Study on Enteric Viruses and Indicators in Surface Water in Kyoto,Japan, During 2014–2015 Season

Certain enteric viruses that are present in the water environment are potential risk factors of waterborne infections. To better understand the impact of viruses in water, both enteric viruses and their potential indicators should be comparatively investigated. In this study, occurrences of GI- and GII-noroviruses (NoVs), sapovirus (SaV), rotavirus (RoV), Aichi virus 1 (AiV-1), enterovirus (EV), and pepper mild mottle virus (PMMoV) were quantitatively determined in surface water samples in Japan. Additionally, the genotype distribution of GI- and GII-NoVs was determined using a next-generation amplicon sequencing. PMMoV was the most abundant virus regardless of season and location, indicating its usefulness as an indicator for the viral contamination of water. Other potential indicators, AiV and EV, were less abundant than GII-NoV. Viruses other than PMMoV showed seasonality, i.e., EV and other viruses (NoVs, SaV, RoV, and AiV-1) became prevalent during summer and winter, respectively. SaV showed a relatively high abundance at a location that was affected by untreated wastewater. Regarding NoV genotypes, GI.1, GI.2, GI.4, GI.5, GI.6, GII.3, GII.4, GII.6, and GII.17 were found from the surface water samples. GII.4 and GII.17 seemed to have contributed to the high abundance of GII-NoV in the samples. Interestingly, GII.17 strains became prevalent in the water samples before becoming prevalent among gastroenteritis patients in Japan. These findings provide further insights into the properties of viruses as contaminants in the water environment.     

The Effect of Heat on the Physicochemical Properties of Bacteriophage MS2

The differences in physicochemical characteristics between infectious and non-infectious viral particles are poorly known. Even for heat, which is known as one of the most efficient treatments to inactivate enteric viruses, the global inactivation mechanisms have not been described yet. Such knowledge would help distinguish between both types of particles and therefore clarify the interpretation of the presence of viral genomes in food after heat treatment. In this study, we examined in particular the differences in electrostatic charge and hydrophobicity between the two particle types. MS2 phage, a common surrogate for enteric viruses, was used as a model virus. The heat-induced inactivation process of the infectious phages caused hydrophobic domains to be transiently exposed and their charge to become less negative. The particles also became progressively permeable to small molecules such as SYPRO Orange dye. The presence of non-infectious phage particles in which the genome was not accessible to RNases has been clearly demonstrated. These observations were done for MS2 phages exposed to a temperature of 60 °C. When exposed to a temperature higher than their critical temperature (72 °C), the particles were disrupted and the genome became available for RNases. At lower temperatures, 60 °C in this study, the transient expression of hydrophobic domains of remaining infectious phages appeared as an interesting parameter for improving their specific detection.     

大连湾和大窑湾表层沉积物病毒分布特点

为了揭示近岸沉积物环境中的病毒-细菌关系,以及探讨病毒对污染环境的响应,本研究利用SYBR Green I染色计数法,分别对2012年5月(春季)、8月(夏季)和11月(秋季)大连湾和大窑湾表层沉积物中的病毒和细菌丰度进行了检测。结果表明:大连湾表层沉积物病毒丰度的季节变化表现为夏季春季秋季,最高值1.59108VLP/g(湿重)出现在夏季;最小值1.53106VLP/g出现在春季。平面分布春季为湾中 湾顶 湾口,夏季和秋季分布特点为湾中 湾口 湾顶。病毒和细菌有显著相关性(R2=0.80,n=20)。而大窑湾表层沉积物病毒丰度的季节变化则变现为夏季秋季春季,最高值7.08107VLP/g出现在夏季,最小值1.16106VLP/g出现在春季。大窑湾区域分为湾内和湾外,3个季节的平面分布均表现为湾外湾内。病毒和细菌的关联性较大连湾差(R2=0.50,n=12)。大连湾及大窑湾表层沉积物病毒与细菌之比分别为4.12和4.09。两个海湾沉积物病毒分布有所差异,可能与沉积物环境有关系,有待进一步研究。     

珠海市中部主要供水水库沉积物重金属时空分布与风险评价

磨刀门和洪湾水道是珠江水系的主要出海口,受潮汐影响,沿线受其调水的凤凰山水库、大镜山水库和竹仙洞水库是粤港澳大湾区珠海市中部的重要饮用水水源地.为了解3座供水水库表层沉积物中的环境质量状况,于2019年丰、枯两季(8月和10月)对库区共15个采样点的8项重金属进行监测,并开展了相关性分析、地累积指数评价、生态风险评估和溯源分析.结果表明,8种重金属在3座水库中的含量平均值大小排序均为：竹仙洞水库>大镜山水库>凤凰山水库.凤凰山水库Hg、 Zn和Pb,大镜山水库Hg、 As、 Mn、 Ni、 Cu、 Zn和Pb,竹仙洞水库8种重金属含量分别超过广东省土壤重金属背景值的1.88～2.75、1.05～2.32和1.69～6.45倍.除凤凰山水库的As,大镜山水库的As和Cu,竹仙洞水库的Cr和Ni外,其余重金属含量均呈现枯水期>丰水期的特征.地累积指数法评价结果表明,3座水库污染程度为：竹仙洞水库>大镜山水库>凤凰山水库.其中,凤凰山水库和大镜山水库仅Hg、 Zn和Pb元素表现为轻度污染,竹仙洞水库整体均受到轻度或偏中度污染.潜在生态风险指数评价结果表明,凤凰山...     

好氧-厌氧两相堆肥过程中抗生素耐药基因的变化特征及影响因素研究

针对堆肥处理过程中抗生素耐药基因（antibiotic resistance genes,ARGs）去除效率不高、诱导潜在致病菌传播扩散等环境安全问题,采用好氧-厌氧两相堆肥处理猪粪、秸秆,探讨ARGs丰度及微生物群落的变化特征,并明确影响ARGs相对丰度变化的关键因子.结果表明:与单一好氧相比,好氧-厌氧两相堆肥能更有效地降低部分ARGs及潜在致病菌的相对丰度,其中ermB、tetK的相对丰度分别降低了39.68%、72.19%,假单胞菌属（Pseudomonas）、梭菌属（Clostridium_sensu_stricto_1）的相对丰度分别降低了96.09%、90.07%.主成分分析（Principal Component Analysis,PCA）及冗余分析（Redundancy analysis,RDA）得出,微生物群落和环境因子均显著影响ARGs相对丰度的变化（P < 0.05）,贡献率分别为82.0%、71.2%.其中,梭菌属（Clostridium_sense_stricto_1）、黄杆菌属（Flavobacterium）、尿素芽孢杆菌属（Ureibacillus）和海洋杆菌属（Oceanobacillus）是影响ARGs相对丰度变化的主要微生物菌属;温度、电导率、含水率和pH是影响ARGs相对丰度变化的关键环境因子,贡献率分别为22.0%、16.7%、16.2%和15.0%.研究显示:与好氧堆肥相比,好氧-厌氧两相堆肥能更有效地去除ARGs,并抑制潜在致病菌的繁殖扩散,从而减少环境风险;然而部分ARGs和潜在致病菌仍存在增殖现象,因此亟需进一步优化好氧-厌氧两相堆肥工艺.      

利用UV-vis及EEMs对比冬季完全混合下两个不同特征水库溶解性有机物的光学特性

结合紫外吸收光谱(UV-vis)与三维荧光光谱技术(EEMs),并利用平行因子分析的方法,对两个混合型水库(周村水库和金盆水库)水体中DOM的来源及差异性进行了分析.结果显示,两个水库水体均存在3个荧光组分,分别为长波类腐殖质(350/460 nm)、可见类富里酸(335/410 nm)和类蛋白(260,285/360 nm).但是两水库水体的DOM荧光强度及组分构成比例均存在显著差异(P0.01),两个水库均以类腐殖质为主,但相比金盆水库,周村水库水体中类腐殖质含量相对较低,类蛋白含量较高.周村水库DOM组分间的相关性大于金盆水库,表明后者的DOM来源更为复杂.通过荧光指数FI,自生源指标BIX,腐殖化指标HIX以及新鲜度指数(β∶α)综合对比表明:冬季,在径流量小的情况下,以耕地、畜牧、居民用地为主,沉积物内源污染严重的周村水库水体的DOM以自生源为主;沿岸以森林生态系统为主的金盆水库的DOM则来自混合输入.结果表明混合型水库水文条件及沿岸生态环境特征是决定DOM来源与特征的关键因素之一.