水体粪便污染的微生物溯源方法研究进展

畜禽粪便和生活污水是造成水体污染的主要因素之一,明确和区分水体污染的来源对污染控制和治理尤为重要.因此,利用微生物进行水体污染的溯源近年来成为国际上的研究热点.本文对两种类型微生物溯源方法的研究现状、优缺点以及应用中存在的问题进行了综述和展望.认为在培养建库微生物溯源方法中重复序列分型应用性最强,而在非培养建库方法中基于大肠杆菌特异性基因的PCR-DGGE具有广阔的应用前景.非培养建库微生物溯源是今后主要的研究方向,培养建库和非培养建库溯源方法相结合才能使溯源结果更加可信.     

分子标记物在禽类粪便污染溯源中的研究及应用进展

排入环境后的禽类粪便不仅会造成水体和土壤环境污染,且其携带的致病菌对人类健康也存在潜在危害,因此快速准确地识别并控制粪便污染源对环境保护和人类健康至关重要。微生物溯源（Microbial source tracking,MST）技术可以利用分子标记物识别人和不同动物的粪便污染,从而有助于及时发现并控制粪便污染。鉴于禽类粪便对环境和人类健康的危害,越来越多的禽类MST标记物被开发并用于禽类的粪便污染溯源研究。归纳总结了多种禽类（如鸡、鸭、鸽子、海鸥、加拿大雁和沙丘鹤等） MST分子标记物及其敏感性和特异性,重点综述了禽类分子标记物的基因来源,包括细菌16S rRNA基因、线粒体DNA和功能基因等。其中,细菌16S rRNA基因在标记物设计中的应用最为广泛,源指示菌主要包括厚壁菌门（Firmicutes）、拟杆菌目（Bacteroidales）、放线菌门（Actinobacteria）、变形菌门（Proteobacteria）和梭杆菌门（Fusobacteria）及其家族成员;以cytb基因、ND5基因、16S rRNA基因和ND2基因等线粒体DNA （Mitochondrial DNA,mtDNA）为设计来源的禽类MST标记物在溯源研究中指示效果最好,具有很大的应用潜能;使用功能基因作为设计来源的禽类MST标记物种类较少,且均表现出较低的敏感性,但是将功能基因作为MST标记物的思路具有一定的参考价值。通过对多种禽类标记物指示效果的比较,能为科研人员快速选择禽类标记物时提供一定的参考。此外,还对禽类MST技术的现存问题进行了分析总结,并对其在我国的发展进行了展望,以期促进MST技术在我国环境质量监测领域中的发展和应用。     

应用肠道微生物示踪地表水粪便污染的研究进展

人和动物的粪便已成为水污染的重要污染源, 严重威胁着饮水安全和经济发展。水质污染微生物的传统检测指示菌是总大肠菌群、粪大肠菌群、埃希大肠菌、肠球菌和梭菌属。经过调查发现, 上述指示菌由于在体外能存活并繁殖, 并且不同宿主之间没有差异性, 不能准确用于追踪污染粪便的来源, 因此该指标难以直接说明粪便污染源和污染程度。最近的研究表明, Faecalibaterium作为水体粪便污染来源追踪的指示微生物具有很多优点。本文综述了粪便污染指示菌以及其相关替代方法在水质检测中的研究进展, 对各种指示菌进行了优、缺点比较, 展望了Faecalibaterium的应用前景。     

黄酒贮存酸败关键微生物的分离鉴定

【背景】贮存陈酿是黄酒生产的重要工艺环节,但由于黄酒中营养物质含量丰富,贮存陈酿过程中时常出现酸败变质的现象,尤其是在大罐的陈酿过程中酸败的发生对黄酒行业造成较大的经济损失。【目的】解析黄酒贮存陈酿过程中造成黄酒酸败的关键微生物,为黄酒贮存酸败微生物的控制提供依据。【方法】采用高通量测序技术分析不同来源酸败黄酒中的主要微生物种类;设计针对性培养基分离培养酸败黄酒中的难培养微生物;设计微生物特异性引物,对16S r RNA基因高度相似的酸败微生物进行区分鉴定;将分离的黄酒酸败微生物接入到未发生酸败的黄酒中验证其生酸能力。【结果】高通量测序技术分析结果显示,酸败黄酒中污染微生物主要为乳酸杆菌属(丰度95%)微生物,在种水平上分析比对结果显示两种难培养微生物[耐酸乳杆菌(Lactobacillus acetotolerans)和食果糖乳杆菌(Lactobacillus fructivorans)]的相对丰度达到了82%以上;采用改进的分离培养基分离出酸败黄酒中的难培养污染微生物36株;利用耐酸乳杆菌rec A基因和食果糖乳杆菌tuf基因的特异性引物准确鉴定出这些微生物菌株为28株耐酸乳杆菌和8株食果糖乳杆菌;将两种主要酸败微生物接入到未发生酸败的黄酒中,培养2周后能够显著提高黄酒酸度。【结论】基于高通量测序的未培养技术可作为食品中难培养污染微生物快速分析的有效方法。基于未培养技术和可培养技术相结合,首次解析并验证黄酒贮存过程中造成黄酒酸败的主要微生物为耐酸乳杆菌和食果糖乳杆菌。     

双歧杆菌黏附的研究进展

双歧杆菌是人体肠道正常菌群中的优势菌种 ,黏附和定植于肠黏膜上皮细胞后 ,对宿主发挥生物屏障、营养、免疫、抗肿瘤、抗衰老等生理作用。黏附 (ａｄｈｅｓｉｏｎ)是指微生物与宿主上皮细胞通过生物化学作用特异性地连接在一起。由于黏附是微生物与微生物、微生物与宿主相互关系的先决条件之一 ,是定植的第一步。因此 ,有关双歧杆菌黏附的研究越来越受到人们的重视。本文现就这一方面的研究进展作一综述。1　双歧杆菌对肠上皮细胞黏附的特点　　双歧杆菌进入肠道后能否黏附于宿主肠道黏膜上皮细胞表面 ,形成稳定的菌群 ,是关系到其是否能发…     

双歧杆菌属特异性测序引物筛选及优化

【背景】目前双歧杆菌的益生功能被普遍认可,越来越多的研究开始关注肠道中双歧杆菌的生物多样性。然而双歧杆菌是肠道中的低丰度物种,现有技术尚难以深入研究其多样性。【目的】基于双歧杆菌16SrRNA基因序列筛选一对适用于分析粪便样品中低丰度双歧杆菌属多样性的特异性引物。【方法】依据已有引物的相对位置及其与双歧杆菌属16S rRNA基因序列的匹配率,将引物重组优化得到扩增片段800 bp的双歧杆菌属特异性引物;通过PCR扩增和琼脂糖凝胶电泳对引物进行实验筛选和特异性验证;以细菌通用引物(27f/1492r)为参照,通过单分子实时(Single-molecule real-time,SMRT)测序技术对不同引物的3份粪便样品中细菌的DNA扩增子进行测序,在种水平上分析比较不同引物的优劣。【结果】对文献中已有的9对双歧杆菌特异性引物进行重组并优化,其中2对引物的理论特异性较好且扩增产物大于800 bp,它们分别为Bif164-f/Pbi R2和Pbi F1/Pbi R2。PCR扩增和琼脂糖凝胶电泳实验发现,Bif164-f/Pbi R2的扩增条带明亮且无拖尾。此外,利用SMRT测序平台对引物27f/1492r和Bif164-f/Pbi R2的3份粪便样品中细菌的DNA扩增子进行测序并分析。27f/1492r扩增子的分析结果显示,3份样品依次分别含1、3、4个双歧杆菌种且双歧杆菌的平均相对含量为0.34%;而Bif164-f/Pbi R2扩增子的分析结果显示,3份样品依次分别含2、6和8个双歧杆菌种且双歧杆菌的平均相对含量为98.72%。上述结果表明,Bif164-f/Pbi R2可在种水平上特异地检出粪便中低丰度的双歧杆菌,进而实现样品中双歧杆菌的多样性分析。【结论】筛选出一对双歧杆菌特异性引物Bif164-f/PbiR2,可在种水平上分析粪便样品中低丰度双歧杆菌的生物多样性,同时也验证了理论结合实验进行引物筛选这种方法的可行性。     

双歧杆菌属特异性定量引物的设计及验证

【目的】旨在设计一对双歧杆菌属特异性引物以检测不同样品中低丰度双歧杆菌的含量。【方法】在NCBI中下载57株双歧杆菌全基因组序列,以其共有单拷贝核心基因为目的片段设计双歧杆菌属特异性引物;并对引物进行PCR初筛和特异性复筛;之后借助ddPCR(Droplet Digital PCR,微滴式数字PCR)依次对筛选出的引物进行特异性、灵敏度和实用性验证。【结果】引物Bif-D-9特异性最好,可扩增出4株双歧杆菌而不能扩增20株非双歧杆菌中的任何一株菌;同时通过ddPCR仪定量稀释后的DNA,其扩增结果呈线性下降趋势,证明其灵敏度较好;另外,Bif-D-9结合ddPCR定量出婴儿粪便中双歧杆菌的拷贝数为71 copies/μL,母亲粪便中双歧杆菌的拷贝数为2.7 copies/μL,证明了该方法的实用性。【结论】引物Bif-D-9具有双歧杆菌属特异性,且灵敏度较高、实用性较好,适用于复杂样品中双歧杆菌属定量。     

禽类特异性引物在珠江三角洲地区的适用性研究

以珠江三角洲地区为目标研究区域, 采集不同地区猪、牛、人、狗、鸽、羊及家禽等72 份粪便样品, 进行DNA 提取, 并选取8 种针对鸡肠道内优势菌群而开发出的特异性引物进行地区适用性验证。结果表明: 粪便DNA 提取试剂盒提取的DNA 纯度符合后续PCR 扩增实验要求。Faecalibaterium 通用引物FAU-F/FAU-R(1^#)检出率为87%(63/72), 对禽类、反刍动物及哺乳动物等都具有较好地检出效果。鸡的特异性Faecalibaterium 引物Fach-F1/Fach-R1、Fach-F2/Fach-R2(2^#、3^#)、特异性短杆菌引物LA35F/LA35R(4^#)、特异性拟杆菌引物chBact-F1/chBact-R16、CP2-9F/CP2-9R(5^#、7^#)灵敏度较差; 鸡的拟杆菌特异性引物qC160F-HU/qBac265R-H(6^#)、鸡的梭状芽胞杆菌特异性引物CP3-49F/CP3-49R(8^#)特异性较差, 在珠江三角洲地区都不具备较好的适用性。然而, 当源解析的目标由鸡扩大至禽类, 6^#及8^#引物的特异性分别提高至81%和72%, 满足珠三角地区禽类粪便污染源解析的适用条件。     

噬菌蛭弧菌生物特性研究进展

本文介绍了噬菌蛭弧菌的培养特性,温度对噬菌蛭弧菌的影响,噬菌蛭弧菌的生化特征,感染宿主的机制,在死的宿主菌中生长的特性,宿主的特异性以及噬菌蛭弧菌对致病菌的生物净化作用等生物特性的研究进展。研究认为,噬菌蛭弧菌是自然环境(水、土壤)中致病微生物的生物拮抗体,且极有可能利用它的寄生和溶解宿主菌细胞的特殊性,对环境水体的生物净化。     

用水体中大肠菌群的含量检测水质污染程度

微生物污染是水质污染的主要原因之一,常用某些与病原微生物有密切关系的微生物的含量来反映水体中病原微生物存在的可能性。水体中病原微生物污染主要来自人畜粪便。因而常选用存在于人体和哺乳动物肠道中的微生物如大肠菌群作为水质污染指示菌。利用指示菌反映水质污染状况具有快速、灵敏的优点。测定大肠菌群含量常用多管发酵法和滤膜法。     

Basin-wide analysis of the dynamics of fecal contamination and fecal source identification in Tillamook Bay, Oregon

The objectives of this study were to elucidate spatial and temporal dynamics in source-specific Bacteroidales 16S rRNA genetic marker data across a watershed; to compare these dynamics to fecal indicator counts, general measurements of water quality, and climatic forces; and to identify geographic areas of intense exposure to specific sources of contamination. Samples were collected during a 2-year period in the Tillamook basin in Oregon at 30 sites along five river tributaries and in Tillamook Bay. We performed Bacteroidales PCR assays with general, ruminant-source-specific, and human-source-specific primers to identify fecal sources. We determined the Escherichia coli most probable number, temperature, turbidity, and 5-day precipitation. Climate and water quality data collectively supported a rainfall runoff pattern for microbial source input that mirrored the annual precipitation cycle. Fecal sources were statistically linked more closely to ruminants than to humans; there was a 40% greater probability of detecting a ruminant source marker than a human source marker across the basin. On a sample site basis, the addition of fecal source tracking data provided new information linking elevated fecal indicator bacterial loads to specific point and nonpoint sources of fecal pollution in the basin. Inconsistencies in E. coli and host-specific marker trends suggested that the factors that control the quantity of fecal indicators in the water column are different than the factors that influence the presence of Bacteroidales markers at specific times of the year. This may be important if fecal indicator counts are used as a criterion for source loading potential in receiving waters.     

Microbial community analysis and identification of alternative host-specific fecal indicators in fecal and river water samples using pyrosequencing

It is important to know the comprehensive microbial communities of fecal pollution sources and receiving water bodies for microbial source tracking. Pyrosequencing targeting the V1-V3 hypervariable regions of the 16S rRNA gene was used to investigate the characteristics of bacterial and Bacteroidales communities in major fecal sources and river waters. Diversity analysis indicated that cow feces had the highest diversities in the bacterial and Bacteroidales group followed by the pig sample, with human feces having the lowest value. The Bacteroidales, one of the potential fecal indicators, totally dominated in the fecal samples accounting for 31%-52% of bacterial sequences, but much less (0.6%) in the river water. Clustering and Venn diagram analyses showed that the human sample had a greater similarity to the pig sample in the bacterial and Bacteroidales communities than to samples from other hosts. Traditional fecal indicators, i.e., Escherichia coli, were detected in the human and river water samples at very low rates and Clostridium perfringens and enterococci were not detected in any samples. Besides the Bacteroidales group, some microorganisms detected in the specific hosts, i.e., Parasutterella excrementihominis, Veillonella sp., Dialister invisus, Megamonas funiformis, and Ruminococcus lactaris for the human and Lactobacillus amylovorus and Atopostipes sp. for the pig, could be used as potential host-specific fecal indicators. These microorganisms could be used as multiple fecal indicators that are not dependent on the absence or presence of a single indicator. Monitoring for multiple indicators that are highly abundant and host-specific would greatly enhance the effectiveness of fecal pollution source tracking.     

Microplate subtractive hybridization to enrich for bacteroidales genetic markers for fecal source identification

The ability to identify sources of fecal pollution plays a key role in the analysis of human health risk and the implementation of water resource management strategies. One approach to this problem involves the identification of bacterial lineages or gene sequences that are found exclusively in a particular host species or group. We used subtractive hybridization to enrich for target host-specific fecal Bacteroidales rRNA gene fragments that were different from those of very closely related reference (subtracter) host sources. Target host rRNA gene fragments were hybridized to subtracter rRNA gene fragments immobilized in a microplate well, and target sequences that did not hybridize were cloned and sequenced for PCR primer design. The use of microplates for DNA immobilization resulted in a one-step subtractive hybridization in which the products could be directly amplified with PCR. The new host-specific primers designed from subtracted target fragments differentiated among very closely related Bacteroidales rRNA gene sequences and distinguished between similar fecal sources, such as elk and cow or human and domestic pet (dog).     

Lachnospiraceae and Bacteroidales alternative fecal indicators reveal chronic human sewage contamination in an urban harbor

The complexity of fecal microbial communities and overlap among human and other animal sources have made it difficult to identify source-specific fecal indicator bacteria. However, the advent of next-generation sequencing technologies now provides increased sequencing power to resolve microbial community composition within and among environments. These data can be mined for information on source-specific phylotypes and/or assemblages of phylotypes (i.e., microbial signatures). We report the development of a new genetic marker for human fecal contamination identified through microbial pyrotag sequence analysis of the V6 region of the 16S rRNA gene. Sequence analysis of 37 sewage samples and comparison with database sequences revealed a human-associated phylotype within the Lachnospiraceae family, which was closely related to the genus Blautia. This phylotype, termed Lachno2, was on average the second most abundant fecal bacterial phylotype in sewage influent samples from Milwaukee, WI. We developed a quantitative PCR (qPCR) assay for Lachno2 and used it along with the qPCR-based assays for human Bacteroidales (based on the HF183 genetic marker), total Bacteroidales spp., and enterococci and the conventional Escherichia coli and enterococci plate count assays to examine the prevalence of fecal and human fecal pollution in Milwaukee's harbor. Both the conventional fecal indicators and the human-associated indicators revealed chronic fecal pollution in the harbor, with significant increases following heavy rain events and combined sewer overflows. The two human-associated genetic marker abundances were tightly correlated in the harbor, a strong indication they target the same source (i.e., human sewage). Human adenoviruses were routinely detected under all conditions in the harbor, and the probability of their occurrence increased by 154% for every 10-fold increase in the human indicator concentration. Both Lachno2 and human Bacteroidales increased specificity to detect sewage compared to general indicators, and the relationship to a human pathogen group suggests that the use of these alternative indicators will improve assessments for human health risks in urban waters.     

Host distributions of uncultivated fecal Bacteroidales bacteria reveal genetic markers for fecal source identification

The purpose of this study was to examine host distribution patterns among fecal bacteria in the order Bacteroidales, with the goal of using endemic sequences as markers for fecal source identification in aquatic environments. We analyzed Bacteroidales 16S rRNA gene sequences from the feces of eight hosts: human, bovine, pig, horse, dog, cat, gull, and elk. Recovered sequences did not match database sequences, indicating high levels of uncultivated diversity. The analysis revealed both endemic and cosmopolitan distributions among the eight hosts. Ruminant, pig, and horse sequences tended to form host- or host group-specific clusters in a phylogenetic tree, while human, dog, cat, and gull sequences clustered together almost exclusively. Many of the human, dog, cat, and gull sequences fell within a large branch containing cultivated species from the genus Bacteroides. Most of the cultivated Bacteroides species had very close matches with multiple hosts and thus may not be useful targets for fecal source identification. A large branch containing cultivated members of the genus Prevotella included cloned sequences that were not closely related to cultivated Prevotella species. Most ruminant sequences formed clusters separate from the branches containing Bacteroides and Prevotella species. Host-specific sequences were identified for pigs and horses and were used to design PCR primers to identify pig and horse sources of fecal pollution in water. The primers successfully amplified fecal DNAs from their target hosts and did not amplify fecal DNAs from other species. Fecal bacteria endemic to the host species may result from evolution in different types of digestive systems.     

Distribution of genetic marker concentrations for fecal indicator bacteria in sewage and animal feces

Very little is known about the density and distribution of fecal indicator bacteria (FIB) genetic markers measured by quantitative real-time PCR (qPCR) in fecal pollution sources. Before qPCR-based FIB technologies can be applied to waste management and public health risk applications, it is vital to characterize the concentrations of these genetic markers in pollution sources (i.e., untreated wastewater and animal feces). We report the distribution of rRNA genetic markers for several general FIB groups, including Clostridium spp., Escherichia coli, enterococci, and Bacteroidales, as determined by qPCR on reference collections consisting of 54 primary influent sewage samples collected from treatment facilities across the United States and fecal samples representing 20 different animal species. Based on raw sewage sample collection data, individual FIB genetic markers exhibited a remarkable similarity in concentration estimates from locations across the United States ranging from Hawaii to Florida. However, there was no significant correlation between genetic markers for most FIB combinations (P > 0.05). In addition, large differences (up to 5 log(10) copies) in the abundance of FIB genetic markers were observed between animal species, emphasizing the importance of indicator microorganism selection and animal source contribution for future FIB applications.     

Survival of host-associated bacteroidales cells and their relationship with Enterococcus spp., Campylobacter jejuni, Salmonella enterica serovar Typhimurium, and adenovirus in freshwater microcosms as measured by propidium monoazide-quantitative PCR

The ideal host-associated genetic fecal marker would be capable of predicting the presence of specific pathogens of concern. Flowthrough freshwater microcosms containing mixed feces and inocula of the pathogens Campylobacter jejuni, Salmonella enterica serovar Typhimurium, and adenovirus were placed at ambient temperature in the presence and absence of diurnal sunlight. The total Enterococcus DNA increased during the early periods (23 h) under sunlight exposure, even though cultivable Enterococcus and DNA in intact cells, as measured by propidium monoazide (PMA), decreased with first-order kinetics during the entire period. We found a significant difference in the decay of host-associated Bacteroidales cells between sunlight exposure and dark conditions (P value < 0.05), whereas the persistence of host-associated Bacteroidales DNA was comparable. The 2-log reduction times of adenovirus were 72 h for sunlight exposure and 99 h for dark conditions with similar decay rate constants (P value = 0.13). The persistences of fecal Bacteroidales cells and Campylobacter cells exposed to sunlight were similar, and host-associated Bacteroidales DNA and waterborne pathogen DNA were degraded at comparable rates (P values > 0.05). Overall, the ratio of quantitative PCR (qPCR) cycle threshold (C(T)) values with and without PMA treatment was indicative of the time elapsed since inoculation of the microcosm with (i) fecal material from different animal sources based on host-associated Bacteroidales and (ii) pure cultures of bacterial pathogens. The use of both PMA-qPCR and qPCR may yield more realistic information about recent sources of fecal contamination and result in improved prediction of waterborne pathogens and assessment of health risk.     

Fecal bacteroidales diversity and decay in response to variations in temperature and salinity

Bacteroidales are attractive as water quality indicators because of their potential to discern sources of fecal pollution, and it is presumed that these bacteria do not multiply outside their host organisms. The persistence of a fecal Bacteroidales marker was monitored over 14 days in river water microcosms that varied in temperature from 10°C to 30°C and salinity from 0‰ to 30‰ by quantitative PCR (qPCR). Decay rates were estimated and compared to the results of other studies examining the survival and persistence of Bacteroidales markers by converting decay rates from other studies to a common decay rate unit. The log-linear decay rates estimated in this work ranged from -0.18 to -1.31 ln(C(T)/C(0)) day(-1), where C(T) is the threshold cycle and C(0) is the concentration of cells at time zero, which is comparable to findings in previous studies. Salinity had a positive effect on Bacteroidales marker persistence, while decay was more rapid at higher temperatures. Comparison of 16S rRNA gene clone libraries generated from microcosm samples indicated that most of the operational taxonomic unit (OTU) and phylogenetic diversity was found within samples and not between samples, indicating at least qualitatively that diverse lineages persist and likely have similar survival characteristics under most of the conditions examined. It was noted that the samples at higher salinities also had the smallest amount of diversity between samples as well as the lowest decay rates. This research also highlights the need for a repository of raw survival and persistence data if more sophisticated models of decay are to be employed and compared between different studies.     

Basin-Wide Analysis of the Dynamics of Fecal Contamination and Fecal Source Identification in Tillamook Bay, Oregon

The objectives of this study were to elucidate spatial and temporal dynamics in source-specific Bacteroidales 16S rRNA genetic marker data across a watershed; to compare these dynamics to fecal indicator counts, general measurements of water quality, and climatic forces; and to identify geographic areas of intense exposure to specific sources of contamination. Samples were collected during a 2-year period in the Tillamook basin in Oregon at 30 sites along five river tributaries and in Tillamook Bay. We performed Bacteroidales PCR assays with general, ruminant-source-specific, and human-source-specific primers to identify fecal sources. We determined the Escherichia coli most probable number, temperature, turbidity, and 5-day precipitation. Climate and water quality data collectively supported a rainfall runoff pattern for microbial source input that mirrored the annual precipitation cycle. Fecal sources were statistically linked more closely to ruminants than to humans; there was a 40% greater probability of detecting a ruminant source marker than a human source marker across the basin. On a sample site basis, the addition of fecal source tracking data provided new information linking elevated fecal indicator bacterial loads to specific point and nonpoint sources of fecal pollution in the basin. Inconsistencies in E. coli and host-specific marker trends suggested that the factors that control the quantity of fecal indicators in the water column are different than the factors that influence the presence of Bacteroidales markers at specific times of the year. This may be important if fecal indicator counts are used as a criterion for source loading potential in receiving waters.     

Terrestrial Sources Homogenize Bacterial Water Quality During Rainfall in Two Urbanized Watersheds in Santa Barbara, CA

Microbiological contamination from runoff is a human health concern in urbanized coastal environments, but the contamination sources are often unknown. This study quantified fecal indicator bacteria and compared the distributions of human-specific genetic markers and bacterial community composition during dry and wet weather in urban creeks draining two neighboring watersheds in Santa Barbara, CA. In a prior study conducted during exclusively dry weather, the creeks were contaminated with human waste as indicated by elevated numbers of the human-specific Bacteroidales marker HF183 (Sercu et al. in Environ Sci Technol 43:293-298, 2009). During the storm, fecal indicator bacterial numbers and loads increased orders of magnitude above dry weather conditions. Moreover, bacterial community composition drastically changed during rainfall and differed from dry weather flow by (1) increased bacterial diversity, (2) reduced spatial heterogeneity within and between watersheds, and (3) clone library sequences more related to terrestrial than freshwater taxa. Finally, the spatial patterns of human-associated genetic markers (HF183 and Methanobrevibacter smithii nifH gene) changed during wet weather, and the contribution of surface soils to M. smithii nifH gene detection was suspected. The increased fecal indicator bacteria numbers during wet weather were likely associated with terrestrial sources, instead of human waste sources that dominated during dry weather flow.