Recently, community ecologists are focusing on the relative importance of local environmental factors and proxies to dispersal limitation to explain spatial variation in community structure. Albeit less explored, temporal processes may also be important in explaining species composition variation in metacommunities occupying dynamic systems. We aimed to evaluate the relative role of environmental, spatial and temporal variables on the metacommunity structure of different organism groups in the Upper Paraná River floodplain (Brazil). We used data on macrophytes, fish, benthic macroinvertebrates, zooplankton, periphyton, and phytoplankton collected in up to 36 habitats during a total of eight sampling campaigns over two years. According to variation partitioning results, the importance of predictors varied among biological groups. Spatial predictors were particularly important for organisms with comparatively lower dispersal ability, such as aquatic macrophytes and fish. On the other hand, environmental predictors were particularly important for organisms with high dispersal ability, such as microalgae, indicating the importance of species sorting processes in shaping the community structure of these organisms. The importance of watercourse distances increased when spatial variables were the main predictors of metacommunity structure. The contribution of temporal predictors was low. Our results emphasize the strength of a trait-based analysis and of better defining spatial variables. More importantly, they supported the view that “all-or- nothing” interpretations on the mechanisms structuring metacommunities are rather the exception than the rule.

Modern metagenomic environmental DNA studies are almost completely reliant on next-generation sequencing, making evaluations of these methods critical. We compare two next-generation sequencing techniques – amplicon and shotgun – on water samples across four of Brazil’s major river floodplain systems (Amazon, Araguaia, Paraná, and Pantanal). Less than 50% of phyla identified via amplicon sequencing were recovered from shotgun sequencing, clearly challenging the dogma that mid-depth shotgun recovers more diversity than amplicon-based approaches. Amplicon sequencing also revealed ~27% more families. Overall the amplicon data were more robust across both biodiversity and community ecology analyses at different taxonomic scales. Our work doubles the sampling size in similar environmental studies, and novelly integrates environmental data (e.g., pH, temperature, nutrients) from each site, revealing divergent correlations depending on which data are used. While myriad variants on NGS techniques and bioinformatic pipelines are available, our results point to core differences that have not been highlighted in any studies to date. Given the low number of taxa identified when coupling shotgun data with clade-based taxonomic algorithms, previous studies that quantified biodiversity using such bioinformatic tools should be viewed cautiously or re-analyzed. Nonetheless, shotgun has complementary advantages that should be weighed when designing projects.

1. It is widely acknowledged that sudden, large-scale flood pulses are drivers of benthic and planktonic biodiversity change in floodplains. The impact of such pulses on pleuston (biotic communities associated with root systems of floating plants) remains to be demonstrated. Here, we investigate the effects of local and regional drivers on seasonal changes in abundance and diversity of ostracod communities in pleuston. 2. Temporal and spatial distribution patterns of species richness, abundance, diversity and evenness of ostracods associated with the floating water hyacinth, Eichhornia crassipes, in a lentic environment from the upper Paraná River floodplain, were investigated in relation to local, as well as regional, environmental factors. Ostracods were sampled monthly over an annual cycle (March 2004-February 2005. Twenty-seven species were found, representing the families Cyprididae, Candonidae, Limnocytheridae and Darwinulidae. Both diversity and abundance of ostracod communities showed seasonal changes, although species turn-over during the year was limited. 3. We tested two hypotheses concerning the causality of these fluctuations: seasonal recruitment and influx of allochthonous ostracods during the flood pulse. Our results indicate that seasonal recruitment is more likely to be the driver of fluctuations in relation to the flood pulse. We postulate that pleuston communities are buffered against possible detrimental effects of flood pulses.

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This study evaluated the differences in composition, abundance and morphology of testate amoebae among different habitats of the same aquatic environment (plankton, aquatic macrophyte and sediment) in the Upper Paraná River floodplain. Triplicate samplings were undertaken monthly at each habitat from April 2007 to March 2008. The structure of the community of testate amoebae was different among the habitats. The species typical for each habitat, according to Indval, were classified by their shell morphology. Arcella species together with Difflugia gramen and Difflugia pseudogramem were more abundant for plankton. Trinema and Phryganella stood out by their abundance and frequency in aquatic macrophytes. Centropyxis was an indicator of sediment. The results indicated a higher frequency of hemispherical and spherical shells in plankton and spherical and elongated shells in aquatic macrophytes. In the sediment, there was a high frequency of elongated species. Our results support the hypothesis that the community of testate amoebae has different structures among the habitats, refuting the idea that the organization of this community in plankton is guided by random events like the resuspension of organisms from the sediment and their displacement from marginal vegetation.Keywords: protists, floodplain lake, aquatic macrophytes, plankton, sediment. Estrutura da comunidade de amebas testáceas em diferentes hábitats em uma planície de inundação neotropical ResumoEste estudo avaliou as diferenças na composição, abundância e morfologia das amebas testáceas entre diferentes hábitats de um mesmo ambiente aquático (plâncton, macrófitas aquáticas e sedimento) da planície de inundação do alto rio Paraná. As amostras foram coletadas mensalmente no período de abril de 2007 a março de 2008. A estrutura da comunidade de amebas testáceas foi diferente entre os hábitats. As espécies típicas para cada hábitat, de acordo com o Indval, foram classificadas pela morfologia da teca. Espécies de Arcella, Difflugia gramen e Difflugia pseudogramem foram mais abundantes para o plâncton. Trinema e Phryganella destacaram-se pela alta abundância e frequência nas macrófitas aquáticas. Centropyxis foi considerado indicador do sedimento. Os resultados indicaram uma alta frequência de tecas esféricas e hemisféricas no plâncton e de tecas alongadas nas macrófitas aquáticas. No sedimento foi registrada uma maior frequência de espécies alongadas. Nossos resultados suportam a hipótese que a comunidade de amebas testáceas possui estrutura diferente entre os hábitats, refutando a ideia que a comunidade presente no plâncton é guiada por processos estocásticos como a ressuspensão dos organismos do sedimento e simples carreamento da vegetação marginal.Palavras-chave: protistas, planície de inundação, macrófitas aquáticas, plâncton, sedimento.

The changes in species composition between habitat patches (beta diversity) are likely related to a number of factors, including environmental heterogeneity, connectivity, disturbance and productivity. Here, we used data from aquatic environments in five Brazilian regions over two years and two seasons (rainy and dry seasons or high and low water level periods in floodplain lakes) in each year to test hypotheses underlying zooplankton beta diversity variation. The regions present different levels of hydrological connectivity, where three regions present lakes that are permanent and connected with the main river, while the water bodies of the other two regions consist of permanent lakes and temporary ponds, with no hydrological connections between them. We tested for relationships between zooplankton beta diversity and environmental heterogeneity, spatial extent, hydrological connectivity, seasonality, disturbance and productivity. Negative relationships were detected between zooplankton beta diversity and both hydrological connectivity and disturbance (periodic dry-outs). Hydrological connectivity is likely to affect beta diversity by facilitating dispersal between habitats. In addition, the harsh environmental filter imposed by disturbance selected for only a small portion of the species from the regional pool that were able to cope with periodic dry-outs (e.g., those with a high production of resting eggs). In summary, this study suggests that faunal exchange and disturbance play important roles in structuring local zooplankton communities.

In freshwater environments, testate amoebae are usually found associated with macrophytes and sediments and many studies have suggested that their occurrence in plankton samples is accidental. This implies that predictable patterns detected in planktonic assemblages should not be observed in testate amoebae assemblages. This hypothesis was tested in this study. Plankton samples were collected from different environments in the Upper Paraná River floodplain. Results show that patterns in species composition and abundance of testate amoebae are predictable, and that dominant species tend to present characteristic shell morphology in hydrologically different environments. We suggest that testate amoebae must be routinely included in plankton ecology studies, at least in floodplain environments.