Sampling the reaches

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.

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).