The general sampling design is shown in Figure 1. Each reach should be visited and sampled twice: during the flowing and non-flowing phases. The non-flowing phase refer to dry riverbeds with or without disconnected pools in the intermittent reach. Details for each sampling protocol are described here.

 Figure 1. Sampling design for the BiodiversIRES project

 Aquatic biodiversity:

For each phase with water (i.e. the flowing phase and non-flowing phases with disconnected pools), collect 4 Surber samples (see details here): 2 Surber samples from 2 riffles and 2 Surber samples from 2 pools from both the intermittent reach and the perennial reach. If the available pools are too small (i.e. < 1 x 1 m), do not consider them.

For each phase with water (see above), collect water for eDNA analyses in 2 pools (for each reach) by passing water through a 0.22 µm filter using Sterivex cartridges (see details here).

During the non-flowing phase, collect sediments from 4 locations (2 from pools and 2 from dry riffles) in the dry riverbed and soils from 4 locations in the adjacent riparian zone (two on each side of the river channel and < 20 m from the riverbed) for seedbank analyses (see details here).

Terrestrial biodiversity:

During both the flowing and non-flowing phases, collect 5 pitfall traps (see details here) in the riverbed at each reach and 5 in the adjacent riparian zone. During the flowing phase, pitfall traps should be placed along the shore.

For each phase, collect 4 sediment samples (dry for non-flowing phases, wet for flowing phases): 2 from pools and 2 from riffles from the riverbed for terrestrial eDNA analysis (see details here). Collect also 4 soil samples from the adjacent riparian zone (two on each side of the river channel and < 20 m from the riverbed).

For the larger fauna, install a photo-trap (see details here) at the site and record the presence of animals over 3 month (or more) during each phase

During the non-flowing phase, in addition to the photo-trap, record animal tracks (see details here).