Trophic downgrading decreases species asynchrony and community stability regardless of climate warming.

Theory and some evidence suggest that biodiversity promotes stability. However, evidence of how trophic interactions and environmental changes modulate this relationship in multitrophic communities is lacking. Given the current scenario of biodiversity loss and climate changes, where top predators are disproportionately more affected, filling these knowledge gaps is crucial. We simulated climate warming and top predator loss in natural microcosms to investigate their direct and indirect effects on temporal stability of microbial communities and the role of underlying stabilising mechanisms. Community stability was insensitive to warming, but indirectly decreased due to top predator loss via increased mesopredator abundance and consequent reduction of species asynchrony and species stability. The magnitude of destabilising effects differed among trophic levels, being disproportionally higher at lower trophic levels (e.g. producers). Our study unravels major patterns and causal mechanisms by which trophic downgrading destabilises large food webs, regardless of climate warming scenarios.

Differently dispersing organism groups show contrasting beta diversity patterns in a dammed subtropical river basin.

Although it is widely known that dams can have large impacts on the environmental and biological characteristics of downstream rivers, there is a substantial lack of studies focusing on which ecological processes cause longitudinal changes in biological communities downstream of reservoirs. We investigated longitudinal patterns in the total beta diversity and its replacement and richness difference components for actively (fish) and passively (phytoplankton) dispersing biological groups. Our results, obtained from a 230 km sampling stretch, demonstrated the key role played by tributaries in the downstream direction from main river impoundment, which influenced local environmental conditions and beta diversity patterns of each biological group. Both replacement and richness difference contributed to high values of total beta diversity for fish (average = 0.77) and phytoplankton (average = 0.79), but their relative importance was more associated with the replacement component for both biological groups (average = 0.45 and 0.52, respectively). Moreover, we observed clear differences between fish and phytoplankton in beta diversity patterns operating at small and broad scales, as well as in the mechanisms driving each beta diversity component. Directional dispersal-related processes and environmental filtering played a major role in shaping total beta diversity and its components for fish, while temporal factors explained considerable parts of phytoplankton beta diversity. Our findings contributed to understanding of tributary-induced heterogeneity and highlight the importance of dam-free stretches of rivers for preserving the integrity of dammed river basins.

Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing.

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.

A Global eDNA Comparison of Freshwater Bacterioplankton Assemblages Focusing on Large-River Floodplain Lakes of Brazil.

With its network of lotic and lentic habitats that shift during changes in seasonal connection, the tropical and subtropical large-river systems represent possibly the most dynamic of all aquatic environments. Pelagic water samples were collected from Brazilian floodplain lakes (total n = 58) in four flood-pulsed systems (Amazon [n = 21], Araguaia [n = 14], Paraná [n = 15], and Pantanal [n = 8]) in 2011-2012 and sequenced via 454 for bacterial environmental DNA using 16S amplicons; additional abiotic field and laboratory measurements were collected for the assayed lakes. We report here a global comparison of the bacterioplankton makeup of freshwater systems, focusing on a comparison of Brazilian lakes with similar freshwater systems across the globe. The results indicate a surprising similarity at higher taxonomic levels of the bacterioplankton in Brazilian freshwater with global sites. However, substantial novel diversity at the family level was also observed for the Brazilian freshwater systems. Brazilian freshwater bacterioplankton richness was relatively average globally. Ordination results indicate that Brazilian bacterioplankton composition is unique from other areas of the globe. Using Brazil-only ordinations, floodplain system differentiation most strongly correlated with dissolved oxygen, pH, and phosphate. Our data on Brazilian freshwater systems in combination with analysis of a collection of freshwater environmental samples from across the globe offers the first regional picture of bacterioplankton diversity in these important freshwater systems.