ABSTRACT:

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].

ABSTRACT:

This study was conducted in the South Fork of King’s Creek at Konza Prairie Biological Station, one of the most well-studied prairie streams in the world. At the USGS gage located on the mainstem (06879560; est. 1979), Kings Creek is a 5th order intermittent stream draining 1059-ha of tallgrass prairie in the Kansas Flint Hills.
This synoptic survey was designed in support of the sampling goals of the Aquatic Intermittency effects on Microbiomes in Streams (AIMS) Project. During June, July, and August 2021, a field team co-collected datasets characterizing the hydrology, biogeochemistry, and ecology across 50 locations within a sub-drainage of the South Fork of Kings’ Creek. The 50 sites were selected to balance multiple competing priorities: (i) strategically targeting existing monitoring infrastructure with long-term data (n=14); (ii) including sites near several known springs and tributary junctions (n=9); and (iii) including a range of drainage area and topographic wetness index (TWI) values (n=27), both of which have been correlated with flow permanence elsewhere. Briefly, the sites selected based on drainage area and TWI were chosen by binning drainage area into 10 bins and then binning TWI into quintiles within each drainage area bin. We then randomly selected a point in each bin after accounting for points selected based on existing infrastructure, springs, and tributaries;, and enforcing a minimum spacing of 100 m between locations. We then made minor adjustments to points to account for field conditions, for instance adjusting locations with respect to a road crossing. For a detailed description of the site selection process, please see (Swenson et al., 2023).