Effects of nutrient and pharmaceutical additions on stream biofilm biomass, function, and community composition

This resource contains the results of an experiment to test the effects of nutrients and pharmaceuticals on stream biofilms at montane and urban sites in the Logan River, Red Butte Creek, and Middle Provo River watersheds located in northern Utah. We constructed contaminant exposure substrates (CES) by filling 1-oz plastic cups with agar amended with individual and combined additions of nutrients (nitrogen, phosphorus, iron) and pharmaceuticals (caffeine, diphenhydramine). The CSV file “treatments_CES” lists the contaminant treatments included in the CES experiment. We capped the agar with an inorganic (fritted glass disc) or organic (cellulose sponge) substrate to select for biofilm assemblages dominated by autotrophic and heterotrophic microbes, respectively, and then deployed CES in the river at each site for 18 - 26 days.

At the end of the deployment period, we used biofilms grown on CES to perform a series of in-stream incubations. We measured respiration and productivity using a modified light-dark bottle incubation method and nitrogen fixation using an acetylene reduction assay. We measured biofilm biomass (chlorophyll a, ash-free dry mass) and calculated Autotrophic Index values (calculated as chlorophyll a concentration divided by ash-free dry mass). The CSV file “biomass_function_CES” contains summary statistics (mean, standard deviation, count) of respiration rates, gross primary production rates, nitrogen fixation rates, chlorophyll a concentrations, ash-free dry mass, and Autotrophic Index values of biofilms on each contaminant treatment and substrate type at our study sites. The Word document “methods_CES” describes the analytical methods used to measure chlorophyll and ash-free dry mass.

To examine microbial community composition of biofilms grown on CES, were used target metagenomics of the 16S rRNA and 18S rRNA genes to identify bacterial and eukaryotic taxa, respectively. The Word document "methods_CES" describes our sequence analysis methods. The folders "bacteria_fastq" and "eukaryotes_fastq" contain the bacterial and eukaryotic fastq files, respectively and the CSV files "bacteria_design_CES" and "eukaryotes_design_CES" describe the contaminant treatment and study location for each sample. The CSV files “bacteria_tax_CES” and “eukaryotes_tax_CES” contain taxonomic classification information for bacterial and eukaryotic OTUs, respectively. The CSV files “bacteria_otu_CES” and “eukaryotes_otu_CES” list the number of sequences of each bacterial and eukaryotic OTU, respectively, in contaminant treatments, with both datasets rarefied to the smallest sample size (bacteria = 27,704 sequences; eukaryotes = 1,523 sequences). The CSV file "bacteria_abun_photo_core_CES" lists bacterial OTUs that were abundant (≥0.1% relative abundance) and rare (<0.1 relative abundance) and potential photoautotrophs and potential heterotrophs. The file also lists bacterial OTUs that were identified as core taxa in each contaminant treatment by land-use combination, where core taxa were defined as OTUs present in at least 75% of samples in a specific grouping.

We characterized light availability, water temperature, and nutrient concentrations at each study site. The Word document "methods_CES" describes our methods for measuring these site characteristics and the analytical methods used to measure nutrient concentrations. The CSV file “site_characteristics_CES” contains percent canopy openness, transmitted incoming PAR, transmitted solar shortwave radiation, degree days, total nitrogen, total phosphorus, ammonium, nitrate, soluble reactive phosphorus, total dissolved iron, and total ferrous iron concentrations at each site.

We examined water column pharmaceutical concentrations at one site on each river using Polar Organic Contaminant Integrative Samplers (POCIS). POCIS were deployed for 20-26 days during summer and fall 2015. The masses of 19 pharmaceuticals which had sorbed onto the POCIS were measured using high performance liquid chromatography combined with tandem mass spectrometry. The CSV file “POCIS_CES” reports concentrations of pharmaceuticals that accumulated in each POCIS (expressed as ng/POCIS) and time-weighted average concentrations of pharmaceuticals (expressed as ng/L), calculated using the resulting pharmaceutical masses and uptake rates reported in the literature. Average daily discharge was calculated using time series discharge data collected by the iUTAH project.

本资源收录了一项实验的结果，旨在检验营养物质和药物对洛根河、红山溪和米德普罗沃河流域山地及城市地区溪流生物膜的影响。我们通过填充含有单一和混合添加的营养物质（氮、磷、铁）及药物（咖啡因、苯海拉明）的琼脂的1盎司塑料杯，构建了污染物暴露底物（CES）。CSV文件“treatments_CES”列出了CES实验中包含的污染物处理。我们使用无机（烧结玻璃圆盘）或有机（纤维素海绵）底物覆盖琼脂，以选择由自养和异养微生物主导的生物膜群落，并将CES部署在每个地点的河流中，持续18至26天。

部署期结束后，我们利用CES上生长的生物膜进行了一系列河流内培养。我们采用改进的光照-黑暗瓶培养法测量呼吸和生产力，以及使用乙炔还原法测量氮固定。我们测量了生物膜生物量（叶绿素a、无灰干燥质量）并计算了自养指数值（计算方法为叶绿素a浓度除以无灰干燥质量）。CSV文件“biomass_function_CES”包含了每个污染物处理和底物类型生物膜在研究地点的呼吸速率、总初级生产力速率、氮固定速率、叶绿素a浓度、无灰干燥质量及自养指数值的汇总统计（平均值、标准差、计数）。Word文档“methods_CES”描述了测量叶绿素和无灰干燥质量的实验方法。

为了研究CES上生长的生物膜的微生物群落组成，我们采用16S rRNA和18S rRNA基因的目标宏基因组学方法分别识别细菌和真核生物分类群。Word文档“methods_CES”描述了我们的序列分析方法。文件夹“bacteria_fastq”和“eukaryotes_fastq”分别包含细菌和真核生物的fastq文件，CSV文件“bacteria_design_CES”和“eukaryotes_design_CES”描述了每个样本的污染物处理和研究地点。CSV文件“bacteria_tax_CES”和“eukaryotes_tax_CES”分别包含细菌和真核生物OTUs的分类学信息。CSV文件“bacteria_otu_CES”和“eukaryotes_otu_CES”分别列出了每个细菌和真核生物OTU在污染物处理中的序列数量，这两个数据集均进行了稀有化处理，以达到最小的样本大小（细菌=27,704序列；真核生物=1,523序列）。CSV文件“bacteria_abun_photo_core_CES”列出了相对丰度较高（≥0.1%）和较低（<0.1相对丰度）的细菌OTUs，以及潜在的化能自养生物和潜在的异养生物。文件还列出了在每种污染物处理和土地利用组合中，被识别为核心分类群的细菌OTUs，其中核心分类群被定义为在特定分组中至少存在于75%的样本中的OTUs。

我们在每个研究地点对光照可用性、水温及营养物质浓度进行了表征。Word文档“methods_CES”描述了测量这些地点特征的方法以及测量营养物质浓度的分析方法。CSV文件“site_characteristics_CES”包含了每个地点的冠层开放度、透射入射光合有效辐射、透射太阳短波辐射、度日数、总氮、总磷、铵、硝酸盐、溶解性活性磷、总溶解铁和总亚铁浓度。

我们使用极性有机污染物综合采样器（POCIS）在每个河流的一个地点检测了水柱中药物的浓度。POCIS在2015年夏季和秋季部署了20至26天。使用高效液相色谱联用串联质谱法测量了吸附在POCIS上的19种药物的量。CSV文件“POCIS_CES”报告了每个POCIS中积累的药物浓度（以ng/POCIS表示）以及使用文献中报道的药物质量和吸收速率计算出的药物时间加权平均浓度（以ng/L表示）。平均每日排放量使用iUTAH项目收集的时间序列排放数据计算得出。