DEEPEND: Microbiome and bacterioplankton rRNA gene sequence data collected from Gulf of Mexico seawater samples. Cruises DP03 and DP04 from Jan 2016 - December 2016

Seawater will be collected and filtered for microbiome and bacterioplankton sequencing and analyses at various depths during planned DEEPEND cruise expeditions to the GOM in 2016. Filters will be stored and then processed for total environmental genomic DNA according to standard methods (see earthmicrobiome.org). 16S rRNA amplicon libraries covering the V4 hypervariable regions will be generated with universal PCR primers and then sequenced on an Illumina MiSeq DNA sequencing platform. Raw paired-end sequences were joined and quality filtered in the bioinformatics program, QIIME. Vertical baseline characterizations will track alpha and beta diversity at different depths ranging from 0 – 1500 m, assess seasonal variation, and examine variation related to nektonic vertical migration. Microbiome analyses will also consider environmental variables unique to the GOM, such as Mississippi river green water inputs, mesoscale features, or microbiomes of associated GOM marine fauna as part of community ecology profiles. When possible, correlations will be made to other environmental factors such as nutrient concentrations.

2016年，在计划开展的前往墨西哥湾（Gulf of Mexico，GOM）的DEEPEND科考航次中，研究人员将采集不同深度的海水并进行过滤，以开展微生物组（microbiome）与浮游细菌（bacterioplankton）的测序与分析工作。过滤所得的滤膜将被妥善保存，随后依据标准流程（详见earthmicrobiome.org）提取总环境基因组DNA。将通过通用PCR引物构建覆盖V4高变区的16S rRNA扩增子文库，随后在Illumina MiSeq DNA测序平台上完成测序。原始双端测序序列将在生物信息学工具QIIME中进行拼接与质量过滤。垂直基线表征工作将对0至1500米不同深度的α多样性与β多样性进行追踪，评估季节变化，并分析与游泳生物垂直迁移相关的群落差异。微生物组分析还将考量墨西哥湾特有的环境变量，例如密西西比河绿水输入、中尺度水文特征，以及墨西哥湾相关海洋动物的微生物组，以此作为群落生态学特征的组成部分。若条件允许，还将尝试建立微生物组与其他环境因子（如营养盐浓度）之间的相关性。