The following standard operating procedure (SOP) was created for the the Aquatic Intermittency effects on Microbiomes in Streams (AIMS), an NSF EPSCoR funded project (OIA 2019603) seeking to explore the impacts of stream drying on downstream water quality across Kansas, Oklahoma, Alabama, Idaho, and Mississippi. AIMS integrates datasets on hydrology, microbiomes, macroinvertebrates, and biogeochemistry in three regions (Mountain West, Great Plains, and Southeast Forests) to test the overarching hypothesis that physical drivers (e.g., climate, hydrology) interact with biological drivers (e.g., biogeochemistry, microbial and macroinvertebrate communities) to control water quality in intermittent streams. An overview of the AIMS project can be found here: https://youtu.be/HDKIBNEnwdM

This protocol details the process for collecting, storing, and routing primary samples for the Microbiome theme. Material for microbiome data analysis from four microhabitat types, i) water, ii) epilithon, iii) benthic sediment, and iv) leaf litter, will be collected during the distributed seasonal sampling (AIMS Approach 2), synoptic sampling (AIMS Approach 3), and the flow manipulation experiment (AIMS Approach 4). All samples will be collected using sterile technique, then subsampled and preserved appropriately for the following downstream laboratory analyses: a) extracellular enzyme activity analysis, b) DNA extraction for 16S rRNA gene and ITS library sequencing and quantitative PCR, c) chlorophyll-a and ash-free dry mass. Those laboratory analyses will be detailed in separate SOPs. This protocol will also include directions for measurement of stream habitat characteristic measurements that are not already covered by biogeochemical and hydrological data collection.
From this SOP, the following data types will be created: field meta-data, extracellular enzyme activity analysis, DNA extraction for 16S rRNA gene and ITS library sequencing and quantitative PCR, chlorophyll-a and ash-free dry mass [AIMS data types: MIME, EEAS, DNAB, DNAF, CHLA, AFDM].