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The possible influence of the continent on the microbiome of the Southwest Atlantic Ocean (SAO) is not yet fully known. The aim of the present study was to evaluate the metagenomic diversity of the SAO nearshore in different locations (e.g., rivers and upwellings) and offshore locations. The studied sites (n = 16) were clustered into four groups (G1-G4) according to the decadal sea surface temperature (SST) and levels of chlorophyll a (chl-a) (2007–2016). G1 (coastal upwelling) presented the highest chl-a values, G2 (shelf) had the highest SST, G3 (offshore north) had the lowest chl-a levels, and G4 (offshore south) was the coldest site. The higher nutrient levels may contribute to higher chl-a-based primary productivity and possibly higher bacterial productivity nearshore. The taxonomic and functional diversity of the total of 16 Illumina shotgun metagenomes were analysed (nearshore: 10, offshore: 6; mean ± standard deviation: 1.87 ± 0.41 million reads per sample). The SAO microbiomes were split into two groups: nearshore and offshore. The SAO coastal zone had higher abundance of picoplanktonic cyanobacteria (e.g., Prochlorococcus), copiotrophic bacteria (e.g., Alteromonas), chl-a photosynthesis, and metabolism of nitrogen and phosphorus. In clear contrast with offshore microbiomes, nearshore microbiomes were heterogenous as a possible effect of riverine runoff and the upwelling. G1 microbiomes had higher abundance of copiotrophic bacteria, while G2 had a higher abundance of Prochlorococcus, and G3 had a higher abundance of Pelagibacter. Offshore metagenomes (G3 and G4) had enrichment of proteorhodopsin light harvesting and sulfur metabolism, possible relevant processes in the SAO. Metagenome assembled genomes (MAGs) demonstrated significant novel microbiome diversity. The most abundant MAGs belong to Flavobacteria and Euryarchaeota. The discrimination of microbial populations and metabolisms in the four studied oceanographic groups provides a first glimpse on the microbial landscape in the SAO.

ABSTRACT The Amazon River watershed and its associated plume comprise a vast continental and oceanic area. The microbial activities along this continuum contribute substantially to global carbon and nutrient cycling, and yet there is a dearth of information on the diversity, abundance, and possible roles of viruses in this globally important river. The aim of this study was to elucidate the diversity and structure of virus assemblages of the Amazon River-ocean continuum. Environmental viral DNA sequences were obtained for 12 locations along the river’s lower reach (n = 5) and plume (n = 7). Sequence assembly yielded 29,358 scaffolds, encoding 82,546 viral proteins, with 15 new complete viral genomes. Despite the spatial connectivity mediated by the river, virome analyses and physical-chemical water parameters clearly distinguished river and plume ecosystems. Bacteriophages were ubiquitous in the continuum and were more abundant in the transition region. Eukaryotic viruses occurred mostly in the river, while the plume had more viruses of autotrophic organisms (Prochlorococcus, Synechococcus) and heterotrophic bacteria (Pelagibacter). The viral families Microviridae and Myoviridae were the most abundant and occurred throughout the continuum. The major functions of the genes in the continuum involved viral structures and life cycles, and viruses from plume locations and Tapajós River showed the highest levels of functional diversity. The distribution patterns of the viral assemblages were defined not only by the occurrence of possible hosts but also by water physical and chemical parameters, especially salinity. The findings presented here help to improve understanding of the possible roles of viruses in the organic matter cycle along the river-ocean continuum. IMPORTANCE The Amazon River forms a vast plume in the Atlantic Ocean that can extend for more than 1,000 km. Microbial communities promote a globally relevant carbon sink system in the plume. Despite the importance of viruses for the global carbon cycle, the diversity and the possible roles of viruses in the Amazon are poorly understood. The present work assesses, for the first time, the abundance and diversity of viruses simultaneously in the river and ocean in order to elucidate their possible roles. DNA sequence assembly yielded 29,358 scaffolds, encoding 82,546 viral proteins, with 15 new complete viral genomes from the 12 river and ocean locations. Viral diversity was clearly distinguished by river and ocean. Bacteriophages were the most abundant and occurred throughout the continuum. Viruses that infect eukaryotes were more abundant in the river, whereas phages appeared to have strong control over the host prokaryotic populations in the plume.

Over the last decade new species of Protozoa have been sequenced and deposited in GenBank. Analyzing large amounts of genomic data, especially using Next Generation Sequencing (NGS), is not a trivial task, considering that researchers used to deal or focus their studies on few genes or gene families or even small genomes. To facilitate the information extraction process from genomic data, we developed a database system called ProtozoaDB that included five genomes of Protozoa in its first version. In the present study, we present a new version of ProtozoaDB called ProtozoaDB 2.0, now with the genomes of 22 pathogenic Protozoa. The system has been fully remodeled to allow for new tools and a more expanded view of data, and now includes a number of analyses such as: (i) similarities with other databases (model organisms, the Conserved Domains Database, and the Protein Data Bank); (ii) visualization of KEGG metabolic pathways; (iii) the protein structure from PDB; (iv) homology inferences; (v) the search for related publications in PubMed; (vi) superfamily classification; and (vii) phenotype inferences based on comparisons with model organisms. ProtozoaDB 2.0 supports RESTful Web Services to make data access easier. Those services were written in Ruby language using Ruby on Rails (RoR). This new version also allows a more detailed analysis of the object of study, as well as expanding the number of genomes and proteomes available to the scientific community. In our case study, a group of prenyltransferase proteinsalready described in the literature was found to be a good drug target for Trypanosomatids.