One sixth of Amazonian tree diversity is dependent on river floodplains.

Amazonia's floodplain system is the largest and most biodiverse on Earth. Although forests are crucial to the ecological integrity of floodplains, our understanding of their species composition and how this may differ from surrounding forest types is still far too limited, particularly as changing inundation regimes begin to reshape floodplain tree communities and the critical ecosystem functions they underpin. Here we address this gap by taking a spatially explicit look at Amazonia-wide patterns of tree-species turnover and ecological specialization of the region's floodplain forests. We show that the majority of Amazonian tree species can inhabit floodplains, and about a sixth of Amazonian tree diversity is ecologically specialized on floodplains. The degree of specialization in floodplain communities is driven by regional flood patterns, with the most compositionally differentiated floodplain forests located centrally within the fluvial network and contingent on the most extraordinary flood magnitudes regionally. Our results provide a spatially explicit view of ecological specialization of floodplain forest communities and expose the need for whole-basin hydrological integrity to protect the Amazon's tree diversity and its function.

Mapping density, diversity and species-richness of the Amazon tree flora.

Using 2.046 botanically-inventoried tree plots across the largest tropical forest on Earth, we mapped tree species-diversity and tree species-richness at 0.1-degree resolution, and investigated drivers for diversity and richness. Using only location, stratified by forest type, as predictor, our spatial model, to the best of our knowledge, provides the most accurate map of tree diversity in Amazonia to date, explaining approximately 70% of the tree diversity and species-richness. Large soil-forest combinations determine a significant percentage of the variation in tree species-richness and tree alpha-diversity in Amazonian forest-plots. We suggest that the size and fragmentation of these systems drive their large-scale diversity patterns and hence local diversity. A model not using location but cumulative water deficit, tree density, and temperature seasonality explains 47% of the tree species-richness in the terra-firme forest in Amazonia. Over large areas across Amazonia, residuals of this relationship are small and poorly spatially structured, suggesting that much of the residual variation may be local. The Guyana Shield area has consistently negative residuals, showing that this area has lower tree species-richness than expected by our models. We provide extensive plot meta-data, including tree density, tree alpha-diversity and tree species-richness results and gridded maps at 0.1-degree resolution.

Long-term Ecological Research: Chasing fashions or being prepared for fashion changes?

Long-term-ecological-research (LTER) faces many challenges, including the difficulty of obtaining long-term funding, changes in research questions and sampling designs, keeping researchers collecting standardized data for many years, impediments to interactions with local people, and the difficulty of integrating the needs of local decision makers with "big science". These issues result in a lack of universally accepted guidelines as to how research should be done and integrated among LTER sites. Here we discuss how the RAPELD (standardized field infrastructure system), can help deal with these issues as a complementary technique in LTER studies, allowing comparisons across landscapes and ecosystems and reducing sampling costs. RAPELD uses local surveys to understand broad spatial and temporal patterns while enhancing decision-making and training of researchers, local indigenous groups and traditional communities. Sampling of ecological data can be carried out by different researchers through standardized protocols, resulting in spatial data that can be used to answer temporal questions, and allow new questions to be investigated. Results can also be integrated into existing biodiversity networks. Integrated systems are the most efficient way to save resources, maximize results, and accumulate information that can be used in the face of the unknown unknowns upon which our future depends.

Unraveling Amazon tree community assembly using Maximum Information Entropy: a quantitative analysis of tropical forest ecology.

In a time of rapid global change, the question of what determines patterns in species abundance distribution remains a priority for understanding the complex dynamics of ecosystems. The constrained maximization of information entropy provides a framework for the understanding of such complex systems dynamics by a quantitative analysis of important constraints via predictions using least biased probability distributions. We apply it to over two thousand hectares of Amazonian tree inventories across seven forest types and thirteen functional traits, representing major global axes of plant strategies. Results show that constraints formed by regional relative abundances of genera explain eight times more of local relative abundances than constraints based on directional selection for specific functional traits, although the latter does show clear signals of environmental dependency. These results provide a quantitative insight by inference from large-scale data using cross-disciplinary methods, furthering our understanding of ecological dynamics.

The Program for Biodiversity Research in Brazil: The role of regional networks for biodiversity knowledge, dissemination, and conservation.

The Program for Biodiversity Research (PPBio) is an innovative program designed to integrate all biodiversity research stakeholders. Operating since 2004, it has installed long-term ecological research sites throughout Brazil and its logic has been applied in some other southern-hemisphere countries. The program supports all aspects of research necessary to understand biodiversity and the processes that affect it. There are presently 161 sampling sites (see some of them at Supplementary Appendix), most of which use a standardized methodology that allows comparisons across biomes and through time. To date, there are about 1200 publications associated with PPBio that cover topics ranging from natural history to genetics and species distributions. Most of the field data and metadata are available through PPBio web sites or DataONE. Metadata is available for researchers that intend to explore the different faces of Brazilian biodiversity spatio-temporal variation, as well as for managers intending to improve conservation strategies. The Program also fostered, directly and indirectly, local technical capacity building, and supported the training of hundreds of undergraduate and graduate students. The main challenge is maintaining the long-term funding necessary to understand biodiversity patterns and processes under pressure from global environmental changes.

Dynamics of mercury in the plankton of a hydroelectric reservoir, Western Amazon.

The energy transfer in the aquatic food chain is an important way for mercury (Hg) to enter other trophic levels. The objective of this work was to evaluate the Hg concentrations in plankton upstream and downstream of the Samuel Hydroelectric Reservoir, Rondônia, Brazil. Phytoplankton and zooplankton samples were collected with 20-µm and 68-µm nylon nets. An aliquot was removed for taxonomic analysis and another for total mercury determination, performed by cold vapor atomic absorption spectroscopy. Water physical-chemical parameters were also measured. The Hg concentrations in total plankton (phytoplankton and zooplankton samples) obtained at the three sampling upstream stations showed the same behavior, with the highest values registered in June 2005 (232 µg kg-1, 118 µg kg-1, 128 µg kg-1). The lowest values at stations J1 and M1 were recorded in November 2005 (4 µg kg-1 and 22 µg kg-1, respectively), while the lowest values at stations M4 and M8 were recorded in October 2005 (22 µg kg-1 and 5 µg kg-1, respectively). The Hg results found in the plankton in this study corroborate the results of other recent studies in the same region. The statistical analyses revealed that Hg concentrations in plankton do not explain the distribution of these organisms at the four sampling stations of Samuel Reservoir. Graphical Abstract.

Biased-corrected richness estimates for the Amazonian tree flora.

Amazonian forests are extraordinarily diverse, but the estimated species richness is very much debated. Here, we apply an ensemble of parametric estimators and a novel technique that includes conspecific spatial aggregation to an extended database of forest plots with up-to-date taxonomy. We show that the species abundance distribution of Amazonia is best approximated by a logseries with aggregated individuals, where aggregation increases with rarity. By averaging several methods to estimate total richness, we confirm that over 15,000 tree species are expected to occur in Amazonia. We also show that using ten times the number of plots would result in an increase to just ~50% of those 15,000 estimated species. To get a more complete sample of all tree species, rigorous field campaigns may be needed but the number of trees in Amazonia will remain an estimate for years to come.

Rarity of monodominance in hyperdiverse Amazonian forests.

Tropical forests are known for their high diversity. Yet, forest patches do occur in the tropics where a single tree species is dominant. Such "monodominant" forests are known from all of the main tropical regions. For Amazonia, we sampled the occurrence of monodominance in a massive, basin-wide database of forest-inventory plots from the Amazon Tree Diversity Network (ATDN). Utilizing a simple defining metric of at least half of the trees ≥ 10 cm diameter belonging to one species, we found only a few occurrences of monodominance in Amazonia, and the phenomenon was not significantly linked to previously hypothesized life history traits such wood density, seed mass, ectomycorrhizal associations, or Rhizobium nodulation. In our analysis, coppicing (the formation of sprouts at the base of the tree or on roots) was the only trait significantly linked to monodominance. While at specific locales coppicing or ectomycorrhizal associations may confer a considerable advantage to a tree species and lead to its monodominance, very few species have these traits. Mining of the ATDN dataset suggests that monodominance is quite rare in Amazonia, and may be linked primarily to edaphic factors.

Species Distribution Modelling: Contrasting presence-only models with plot abundance data.

Species distribution models (SDMs) are widely used in ecology and conservation. Presence-only SDMs such as MaxEnt frequently use natural history collections (NHCs) as occurrence data, given their huge numbers and accessibility. NHCs are often spatially biased which may generate inaccuracies in SDMs. Here, we test how the distribution of NHCs and MaxEnt predictions relates to a spatial abundance model, based on a large plot dataset for Amazonian tree species, using inverse distance weighting (IDW). We also propose a new pipeline to deal with inconsistencies in NHCs and to limit the area of occupancy of the species. We found a significant but weak positive relationship between the distribution of NHCs and IDW for 66% of the species. The relationship between SDMs and IDW was also significant but weakly positive for 95% of the species, and sensitivity for both analyses was high. Furthermore, the pipeline removed half of the NHCs records. Presence-only SDM applications should consider this limitation, especially for large biodiversity assessments projects, when they are automatically generated without subsequent checking. Our pipeline provides a conservative estimate of a species' area of occupancy, within an area slightly larger than its extent of occurrence, compatible to e.g. IUCN red list assessments.

Chromium distribution in an Amazonian river exposed to tannery effluent.

This study aims to evaluate the Cr concentrations in surface water, suspended particles, and bottom sediments exposed to tannery effluent releases in the Candeias River. Cr concentrations were compared in relation to environmental thresholds imposed by United States Environmental Protection Agency (USEPA) and the Brazilian Environmental Council (CONAMA), and the geoaccumulation index (Igeo) was calculated in bottom sediment. Samples were collected in flood and dry seasons. Cr extraction was done by an acid extraction and quantified by flame atomic absorption spectrometry. Most samples were found to be below the environmental thresholds imposed by CONAMA and USEPA, except in the one from the discharge zone sampled during the dry season, showing values 1.5 and 6.1 higher than CONAMA in water and bottom sediment, respectively. Cr concentrations were significantly higher (P < 0.001) in suspended particles during dry season than flood season. Surface water and bottom sediment did not show significant differences between the seasons. The Igeo revealed an enrichment of Cr in bottom sediments after discharge zone, indicating that the effluent may be contributing to metal accumulation in the sediment. Apparently, the Candeias River shows a wash behavior on the river bottom, leaching the accumulated metal deposited on the riverbed to other areas during the flood pulses, which decreases Cr concentration in the discharge zone during dry seasons. Thus, this behavior can promote Cr dispersion to unpolluted areas.

Estimating the global conservation status of more than 15,000 Amazonian tree species.

Estimates of extinction risk for Amazonian plant and animal species are rare and not often incorporated into land-use policy and conservation planning. We overlay spatial distribution models with historical and projected deforestation to show that at least 36% and up to 57% of all Amazonian tree species are likely to qualify as globally threatened under International Union for Conservation of Nature (IUCN) Red List criteria. If confirmed, these results would increase the number of threatened plant species on Earth by 22%. We show that the trends observed in Amazonia apply to trees throughout the tropics, and we predict that most of the world's >40,000 tropical tree species now qualify as globally threatened. A gap analysis suggests that existing Amazonian protected areas and indigenous territories will protect viable populations of most threatened species if these areas suffer no further degradation, highlighting the key roles that protected areas, indigenous peoples, and improved governance can play in preventing large-scale extinctions in the tropics in this century.

Flood pulse and spatial dynamics of mercury in sediments in Puruzinho lake, Brazilian Amazon / O pulso de inundação e a dinâmica espacial do mercúrio em sedimentos no lago Puruzinho, Amazônia Brasileira

The study was conducted in Puruzinho lake (Humaitل, AM) considering seasonal periods of rainy and dry in way to elucidate the flood pulse importance in the deposition, remobilization and distributions of mercury and organic matter in bottom sediments in the Madeira River Basin (Brazilian Amazon). Bottom sediments and soils samples were analyzed for total mercury and organic matter. Mercury concentrations obtained in bottom sediment were 32.20-146.40 ng g-1 and organic matter values were 3.5 - 18.0%. The main region for accumulation of mercury and organic matter was in the central and deepest lake area In the rainy season there was a greater distribution of Hg and organic matter, mainly controlled by means of income of the Madeira river water during flooding, while the predominant process in the dry season was the remobilization of total Hg due to the resuspension of bottom sediments.

Este estudo foi realizado no lago Puruzinho (Humaitá, AM) considerando os períodos de cheia e seca para investigar a importância do pulso de inundação na deposição, remobilização e distribuição das concentrações de mercúrio e matéria orgânica nos sedimentos de fundo no lago da bacia do rio Madeira, na Amazônia brasileira. As amostras de sedimentos e solos foram analisadas para mercúrio total e matéria orgânica. As concentrações mercúrio no sedimento de fundo variaram entre 32,20 e 146,40 ng g-1 e as porcentagens de matéria orgânica variaram de 3,5 a 18,0%. A principal região de acumulação de mercúrio e de matéria orgânica foi na área central e mais profunda do lago. Na estação chuvosa ocorreu maior distribuição de Hg e de matéria orgânica controlada principalmente pelo pulso de inundação do rio Madeira, enquanto que no período de seca predominam os processos de remobilização de mercúrio devido a resssuspensão do sedimento de fundo.