Inter-annual variability of rainfalls in the Amazon basin and its vicinity

An analysis of the rainfall series (12-month running means) of the 5° × 5° gridded data in the Amazon river basin and its vicinity (15° N – 20° S, 30° - 80° W) indicated that the rainfalls were highly variable both from year to year and from region to region. Correlations with even nearby regions hardly exceeded 0.50, though correlations were better (up to 0.70) in the regions near the eastern coast of Brazil. Moderate relationship with ENSO indices was obtained for the Amazon river basin and the regions to its north, and for NE Brazil, while moderate relationship with South Atlantic SST was obtained for NE Brazil and the region immediately to its west. All other relationships (with 30 hPa wind, North Atlantic Oscillation Index, etc.) were obscure.

Genome assembly and annotation of the tambaqui (Colossoma macropomum): an emblematic fish of the Amazon River basin

ABSTRACTColossoma macropomum known as “tambaqui” is the largest Characiformes fish in the Amazon River Basin and a leading species in Brazilian aquaculture and fisheries. Good quality meat and great adaptability to culture systems are some of its remarkable farming features. To support studies into the genetics and genomics of the tambaqui, we have produced the first high-quality genome for the species. We combined Illumina and PacBio sequencing technologies to generate a reference genome, assembled with 39X coverage of long reads and polished to a QV=36 with 130X coverage of short reads. The genome was assembled into 1,269 scaffolds to a total of 1,221,847,006 bases, with a scaffold N50 size of 40 Mb where 93% of all assembled bases were placed in the largest 54 scaffolds that corresponds to the diploid karyotype of the tambaqui. Furthermore, the NCBI Annotation Pipeline annotated genes, pseudogenes, and non-coding transcripts using the RefSeq database as evidence, guaranteeing a high-quality annotation. A Genome Data Viewer for the tambaqui was produced which benefits any groups interested in exploring unique genomic features of the species. The availability of a highly accurate genome assembly for tambaqui provides the foundation for novel insights about ecological and evolutionary facets and is a helpful resource for aquaculture purposes.

Patterns of Pelagic Fish Diversity in Floodplain Lakes of Whitewater and Blackwater Drainage Systems Within the Central Amazon River Basin of Brazil

The Amazon River Basin, one of the world’s most threatened ecosystems, has an enormous diversity of fish species, a result of temporally and spatially complex habitat containing biogeochemically different river systems. The annual hydrologic cycle results in floodplain lakes during low water and inundates forests during high water, exposing fish to different resources and environmental conditions. The two principal river systems in the central Brazilian Amazon are blackwater, with nutrient-poor acidic water, and nutrient-rich whitewater. Although species-rich, the Amazon Basin is data-poor in terms of comparative studies on a regional scale. We analyzed data sets from independent sampling studies of pelagic fish in 16 floodplain lakes, nine whitewater (Rio Solimões) and seven blackwater (Rio Negro), in the central Amazon Basin of Brazil. Our findings suggest striking similarities in pelagic fish diversity patterns. Species richness was virtually equal (165 in whitewater and 168 in blackwater). Both species richness, and number of migratory species, per lake increased toward the confluence of the rivers in both systems in our study. The proportion of unique species was also similar in whitewater lakes and blackwater (41 and 43%, respectively), boosting total regional richness to 237 species. However, species composition in whitewater lakes was more homogenous (lower β diversity), and species composition was associated with conductivity and pH in whitewater, but with dissolved oxygen and transparency in blackwater. Therefore, regional fish diversity cannot be represented by sampling one lake or even one drainage system, but must include multiple lakes from both systems. These two systems may differ in sensitivity to anthropogenic stressors such as damming and deforestation.

In-stream turbines for sustainable hydropower development in the Amazon river basin

<p>Given the ongoing and planned hydropower development projects in the Amazon River basin, appalling losses in biodiversity, river ecology and river connectivity are inevitable. These hydropower projects are proposed to be built in exceptionally endemic sites, setting records in environmental losses by impeding fish movement, altering flood pulse, causing large-scale deforestation, and increasing greenhouse gas emissions. With the burgeoning energy demand combined with the aforementioned negative impacts of conventional hydropower technology, there is an imminent need to re-think the design of hydropower to avoid the potentially catastrophic consequences of large dams. It is certain that the Amazon will undergo some major hydrological changes in the near future because of the compounded effects of climate change and proposed dams, if built with the conventional hydropower technology. In this study, we present a transformative hydropower outlook that integrates low-head hydropower technology (e.g., in-stream turbines) and multiple environmental aspects, such as river ecology and protected areas. We employ a high resolution (~2km) continental scale hydrological model called LEAF-Hydro-Flood (LHF) to assess the in-stream hydropower potential in the Amazon River basin. We particularly focus on quantifying the potential and feasibility of employing instream turbines in the Amazon instead of building large dams. We show that a significant portion of the total energy planned to be generated from conventional hydropower in the Brazilian Amazon could be harnessed using in-stream turbines that utilize kinetic energy of water without requiring storage. Further, we also find that implementing in-stream turbines as an alternative to large storage-based dams could prove economically feasible, since most of the environmental and social costs associated with dams are eliminated. Our results open multiple pathways to achieve sustainable hydropower development in the Amazon to meet the ever-increasing energy demands while minimizing hydrological, social, and ecological impacts. It also provides important insight for sustainable hydropower development in other global regions. The results presented are based on a manuscript under revision for Nature Sustainability.</p>

A New Variant B Chromosome in Auchenipteridae: The Role of (GATA)n and (TTAGGG)n Sequences in Understanding the Evolution of Supernumeraries in Trachelyopterus

Basic and molecular cytogenetic techniques were carried out in 3 Neotropical region populations of catfishes, two of Trachelyopterus galeatus (one from the marshlands of Paraguay River basin and another from Lago Catalão, Amazon River basin) and one of Trachelyopterus porosus, a sympatric population to T. galeatus from the Amazon River basin. This study aimed to describe and understand the structure and evolution of Trachelyopterus B chromosomes, mainly through physical mapping of repetitive elements. A diploid number of 58 chromosomes was found for all individuals, as well as the presence of B chromosomes. For T. porosus this is the first report of a supernumerary. The sympatric species of T. galeatus and T. porosus from Amazon River had 1–3 B chromosomes and T. galeatus from Paraguay River had 1–2 B chromosomes, all of them showed intra- and interindividual numerical variation. Two females of T. porosus exhibited a new variant B chromosome (B2), previously not seen in Auchenipteridae, which might have originated from B1 chromosomes. All B chromosomes were entirely heterochromatic. In contrast to all complement A and B2 chromosomes, in which the telomeric sequences were found in the telomeric regions, B1 chromosomes of all populations were totally marked by (TTAGGG)n probes. (GATA)n sequence sites were found through all complement A chromosomes, but B1 and B2 chromosomes exhibited only a clustered block in one of the chromosome arms. The most frequent B chromosomes (B1) in all populations/species, including those previously studied in Auchenipteridae catfishes, share the following characteristics: totally heterochromatic, small, metacentric, with accumulation of repetitive (TTAGGG)n sequences, and a low number of (GATA)n copies, which might suggest a common ancient origin in Trachelyopterus species/populations.

Genetic Diversity and Potential Paths of Transmission of Mycobacterium bovis in the Amazon: The Discovery of M. bovis Lineage Lb1 Circulating in South America

Bovine tuberculosis (bTB) has yet to be eradicated in Brazil. Herds of cattle and buffalo are important sources of revenue to people living in the banks of the Amazon River basin. A better understanding of Mycobacterium bovis (M. bovis) populational structure and transmission dynamics affecting these animals can significantly contribute in efforts to improve their sanitary status. Herein, we sequenced the whole genome of 22 M. bovis isolates (15 from buffalo and 7 from cattle) from 10 municipalities in the region of the Lower Amazon River Basin in Brazil and performed phylogenomic analysis and Single Nucleotide Polymorphism (SNP)-based transmission inference to evaluate population structure and transmission networks. Additionally, we compared these genomes to others obtained in unrelated studies in the Marajó Island (n = 15) and worldwide (n = 128) to understand strain diversity in the Amazon and to infer M. bovis lineages. Our results show a higher genomic diversity of M. bovis genomes obtained in the Lower Amazon River region when compared to the Marajó Island, while no significant difference was observed between M. bovis genomes obtained from cattle and buffalo (p ≥ 0.05). This high genetic diversity is reflected by the weak phylogenetic clustering of M. bovis from the Lower Amazon River region based on geographic proximity and in the detection of only two putative transmission clusters in the region. One of these clusters is the first description of inter-species transmission between cattle and buffalo in the Amazon, bringing implications to the bTB control program. Surprisingly, two M. bovis lineages were detected in our dataset, namely Lb1 and Lb3, constituting the first description of Lb1 in South America. Most of the strains of this study (13/22) and all 15 strains of the Marajó Island carried no clonal complex marker, suggesting that the recent lineage classification better describe the diversity of M. bovis in the Amazon.

Long-Term Spatiotemporal Variation of Droughts in the Amazon River Basin

The Amazon River Basin (ARB) plays an important role in the hydrological cycle at the regional and global scales. According to the Intergovernmental Panel on Climate Change (IPCC), the incidence and severity of droughts could increase in this basin due to human-induced climate change. Therefore, the assessment of the impacts of extreme droughts in the ARB is of vital importance to develop appropriate drought mitigation strategies. The purpose of this study is to provide a comprehensive characterization of dry spells and extreme drought events in terms of occurrence, persistence, spatial extent, severity, and impacts on streamflow and vegetation in the ARB during the period 1901–2018. The Standardized Precipitation-Evapotranspiration Index (SPEI) at multiple time scales (i.e., 3, 6, and 12 months) was used as a drought index. A weak basin-wide drying trend was observed, but there was no evidence of a trend in extreme drought events in terms of spatial coverage, intensity, and duration for the period 1901–2018. Nevertheless, a progressive transition to drier-than-normal conditions was evident since the 1970s, coinciding with different patterns of coupling between the El Niño/Southern Oscillation (ENSO) phenomenon and the Pacific Decadal Oscillation (PDO), Atlantic Multidecadal Oscillation (AMO), and Madden–Julian Oscillation (MJO) as well as an increasing incidence of higher-than-normal surface air temperatures over the basin. Furthermore, a high recurrence of short-term drought events with high level of exposure to long-term drought conditions on the sub-basins Ucayali, Japurá-Caquetá, Jari, Jutaí, Marañón, and Xingu was observed in recent years. These results could be useful to guide social, economic, and water resource policy decision-making processes in the Amazon basin countries.