Explaining the mechanisms underlying spatial and temporal variation in community composition is a major challenge. Nevertheless, the processes controlling temporal variation at a site (i.e., temporal β-diversity, including its turnover and nestedness components) are less understood than those affecting variation among sites (i.e., spatial β-diversity). Short-term temporal turnover (e.g., throughout an annual cycle) is expected to correlate positively with seasonal environmental variability and landscape connectivity, but also species pool size (γ-diversity). We use the megadiverse Amazonian freshwater ichthyofauna as a model to ask whether seasonality and landscape connectivity drive variation in temporal species turnover among geomorphological habitat types, while accounting for between-habitat variation in γ-diversity. 11,397 fish representing 260 species were collected during a year-long sampling program from an area containing the lowland Amazon’s four major geomorphological habitat types: rivers, floodplains, terra firme streams, and shield streams. River-floodplain systems exhibit strong but predictable seasonality (via a high-amplitude annual flood pulse), high connectivity, and high species richness with many rare species. Terra firme and shield streams exhibit low seasonality, low connectivity, and low species richness with proportionally fewer rare species. Based on these parameters we predicted that river-floodplain systems should have higher temporal turnover than stream systems. Using a null model approach combined with β-deviation calculations, we confirmed that rivers and floodplains do exhibit higher turnover (but not nestedness) than terra firme and shield streams, even when controlling for the potentially confounding effect of higher species richness in river-floodplain systems. All habitats exhibit low temporal nestedness, indicating that short-term changes in community composition result primarily from temporal species turnover. Our results provide a timely reminder that efforts to conserve the Amazon’s threatened aquatic biodiversity should account for the distinct temporal dynamics of habitat types and variation in hydrological seasonality.

We studied one of the few Amazonian regions where all four geomorphological habitats occur in close proximity (near Santarém, Brazil, Fig. 1d). This lower Amazon region also includes river-floodplain systems belonging to the three distinct biogeochemical water types of the Amazon basin: nutrient-poor, humic-stained ‘blackwaters’  (BW); nutrient-poor ‘clearwaters’ (CW); and nutrient rich, sediment-laden ‘whitewaters’  (WW) (Sioli 1984, Bogotá-Gregory et al., 2020). We estimated temporal β-diversity for rivers-floodplain systems in all three water types, allowing us to evaluate whether water type, as well as geomorphological habitat type, influence rates of temporal turnover and nestedness.

We sampled 16 sites (Fig. 1d) every two months through a complete annual hydrological cycle, beginning October 2014: Rivers: two river-margin sites in the BW River (R.) Arapiuns (BR1, BR2), two in the CW R. Tapajós (CR1, CR2), and two in the WW R. Amazonas (WR1, WR2); Floodplains: two floodplain lake sites in the BW R. Arapiuns (BF1, BF2), two in the CW R. Tapajós (CF1, CF2), and two in the WW R. Amazonas (WF1, WF2); Terra firme streams: two sites in the lowland terra firme peneplain (Cretaceous Alter do Chão formation) (TS1, TS2); Shield streams: two sites in the upland Paleozoic shield (Devonian Ererê formation) (SS1, SS2). Hence our sampling design comprised eight geomorphological habitat/water type combinations, each replicated at two sites, and sampled six times through the year for a planned total of 96 sampling events. TS1 and TS2 were sampled only five times due to logistical challenges during the first sampling event, and BF2 and WR2 were sampled only five times due to severe weather at the first event for BF2 and fifth for WR2. Thus, the actual number of sampling events was 92.
The river-floodplain habitats exhibited a flood cycle of ca. 5 m amplitude, with an April-July high-water period and October-December low-water period. Year-long variation in water levels in the shield and terra firme streams is < 0.5 m (except briefly after heavy rain) in response to local rainfall – with a December-June wet season followed by a dry season. We selected permanent floodplain lakes of similar size (BF1, 0.17 km2; BF2, 0.25 km2; CF1, 0.18 km2; CF2, 0.21 km2; WF1, 0.18 km2, WF2, 0.26 km2; Fig. 1d) and permanent terra firme and shield streams of similar sizes (3-6 m wide, to 1 m deep). All 16 sites were surrounded by relatively well-protected natural forest.

Due to habitat heterogeneity, it was impossible to use the same gear and sample technique in all habitat types. Therefore, for each habitat we used the gear considered to obtain a representative sampling and then standardized for effort within a given habitat type across all sampling events in the annual cycle. To maximize sampled species diversity in river and floodplain sites, we sampled with gill nets deployed ca. 30 m from the shoreline in batteries of four (25 x 3 m, 15, 30, 45, 60 mm mesh) from 6 am to 9 am and from 6 pm to 9 pm. In the much smaller habitat volumes of terra firme and shield streams, we used three gear types, each with a timed effort of 2 hours/sampling event during daylight hours: a 1.5 x 6 m seine net (5 mm mesh) in deeper pools; a 2.0 x 1.1 m bag-seine (2 mm mesh) in riffles and margins; a dipnet (Expedition Hex-Trapnet, Duraframe Dipnet, Viola WI, with 3 mm mesh and 30 cm bag depth), used with the aid of an electric fish finder (Haag et al. 2019), in leaf litter and marginal root mats; the dipnet-electric fish finder combination sampled gymnotiform electric fish and other nocturnally active fish hiding in the substrate. For each stream, all gear types were used along a 100 m stretch in a downstream-upstream direction with the ends of the section blocked with net panels to minimize escape. Fish were euthanized with 600 mg L-1 eugenol, preserved, and deposited at the biodiversity collections listed in Supporting Information Appendix S1. We identified specimens using species descriptions and keys from the taxonomic literature. 

Measuremens of physicochemical water parameters follow: 
Bogotá-Gregory, J.D., Lima, F.C.T., Correa, S.B., Silva-Oliveira, C., Jenkins, D., Ribeiro, F.R., Lovejoy, N.R., Reis, R.E. & Crampton, W.G.R. (2020) Biogeochemical water type influences community composition, species richness, and biomass in megadiverse Amazonian fish assemblages. Scientific Reports, 10, 15349.