Brumadinho dam collapse induces changes in the microbiome and the antibiotic resistance of the Paraopeba River (Minas Gerais, Brazil).

The rupture of the Córrego do Feijão dam in Brumadinho (January 25, 2019) caused serious damage to the Paraopeba River and compromised the quality of its waters for human consumption. However, the possible effects of the dam collapse on the river microbiome and its antibiotic resistance profiles are unknown. The present study aims to analyse the possible shifts in microbial diversity and enhancement of antibiotic resistance in the Paraopeba River. To this end, two sampling campaigns (February and May 2019) were performed to obtain water across the entire Paraopeba River (eight sampling locations: Moeda, Brumadinho, Igarapé, Juatuba, Varginha, Angueretá, Retiro Baixo and Três Marias; ~464 km). This sampling scheme enabled determining the effects of the disaster on the river microbiome. Total DNA and microbial isolation were performed with these water samples. The 16S rRNA-based microbiome analyses (n = 24; 2.05 million 16S rRNA reads) showed changes in microbial diversity immediately after the disaster with the presence of metal-indicating bacteria (Acinetobacter, Bacillus, Novosphingobium, and Sediminibacterium). Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) identification of bacterial isolates (n = 170) also disclosed possible indicators of faecal contamination across the Paraopeba (Cloacibacterium, Bacteroides, Feaecalibacterium, Bifidobacterium, Citrobacter, Enterobacter, Enterococcus and Escherichia). Antibiotic resistance increased significantly to ampicillin, ampicillin/sulbactam, amoxicillin/clavulanate, ceftriaxone, and cefalotin among isolates obtained in May after the disaster. The effects of toxic mud on microbiomes were felt at all points sampled up to Anguereta. The ore mud may have exacerbated the growth of different antibiotic-resistant, metal-resistant, and faecal-indicating bacteria in the Paraopeba River.

Vibrio fluminensis sp. nov. isolated from the skin of Southern Atlantic sharpnose-pufferfish (Canthigaster figueiredoi).

This manuscript provides the description of the bacterial strain A621T characterized by Gram negative motile rods, presenting green circular colonies on TCBS. It was obtained from the skin of the sharpnose pufferfish Canthigaster figueredoi (Tetraodontidae Family), collected in Arraial do Cabo, located in the Rio de Janeiro region, Brazil. Optimum growth occurs at 20-28 °C in the presence of 3% NaCl. The Genome sequence of the novel isolate consisted of 4.224 Mb, 4431 coding genes and G + C content of 44.5%. Genomic taxonomy analysis based on average amino acid (AAI), genome-to-genome-distance (GGDH) and phylogenetic reconstruction placed (A621T= CBAS 741T = CAIM 1945T = CCMR 150T) into a new species of the genus Vibrio (Vibrio fluminensis sp. nov). The genome of the novel species contains four gene clusters (~ 56.17 Kbp in total) coding for different types of bioactive compounds that hint to several possible ecological roles in the sharpnose pufferfish host.

Sponges present a core prokaryotic community stable across Tropical Western Atlantic.

Sponges are among the earliest lineages of metazoans, with first fossil records dated back to 890 million years ago. All sponge species present associations with microorganisms to some extension, which influence sponges' survival and adaptation. Sponge species can be divided into two categories, Low Microbial Abundance and High Microbial Abundance, depending on the abundance of the microbial community that they host. Monanchora arbuscula (a Low Microbial Abundance sponge species) and Xestospongia muta (a High Microbial Abundance sponge species) are sponges with widespread distribution in the Tropical Western Atlantic. Despite previous studies on the major features of these species, little is known whether M. arcuscula and X. muta prokaryotic communities are stable across vast geographic regions. We obtained a total of ~9.26 million 16S rRNA gene Illumina sequences for M. arbuscula samples collected at seven locations and for X. muta samples collected at three locations, corresponding to five ecoregions of the Caribbean and the Southwestern Atlantic (N = 105, 39 from M. arcuscula and 66 from X. muta). These samples reflected different ecological strategies for prokaryotic communities assembly, since the core prokaryotic communities of M. arbuscula are more heterotrophic and shared with different sources (corals, sponges, seawater, sediments), while X. muta has more significant photosynthetic prokaryotic communities, mainly outsourced from other sponges. Results of M. arbuscula and X. muta prokaryotic communities analysis demonstrate that both sponge species have core prokaryotic communities stable across a vast geographic area (> 8000 km), and the world's most notable coastal marine biogeographic filter, the Amazon River Mouth, in spite of the significant differences found among transient prokaryotic communities of both sponge species.

Metaphor-A workflow for streamlined assembly and binning of metagenomes.

Recent advances in bioinformatics and high-throughput sequencing have enabled the large-scale recovery of genomes from metagenomes. This has the potential to bring important insights as researchers can bypass cultivation and analyze genomes sourced directly from environmental samples. There are, however, technical challenges associated with this process, most notably the complexity of computational workflows required to process metagenomic data, which include dozens of bioinformatics software tools, each with their own set of customizable parameters that affect the final output of the workflow. At the core of these workflows are the processes of assembly-combining the short-input reads into longer, contiguous fragments (contigs)-and binning, clustering these contigs into individual genome bins. The limitations of assembly and binning algorithms also pose different challenges depending on the selected strategy to execute them. Both of these processes can be done for each sample separately or by pooling together multiple samples to leverage information from a combination of samples. Here we present Metaphor, a fully automated workflow for genome-resolved metagenomics (GRM). Metaphor differs from existing GRM workflows by offering flexible approaches for the assembly and binning of the input data and by combining multiple binning algorithms with a bin refinement step to achieve high-quality genome bins. Moreover, Metaphor generates reports to evaluate the performance of the workflow. We showcase the functionality of Metaphor on different synthetic datasets and the impact of available assembly and binning strategies on the final results.

Breviolum and Cladocopium Are Dominant Among Symbiodiniaceae of the Coral Holobiont Madracis decactis.

The scleractinian reef building coral Madracis decactis is a cosmopolitan species. Understanding host-symbiont associations is critical for assessing coral's habitat requirements and its response to environmental changes. In this study, we performed a fine grained phylogenetic analyses of Symbiodiniaceae associated with Madracis in two locations in the Southwest Atlantic Ocean (Abrolhos Bank and St. Peter and St. Paul Archipelago). Previous studies have argued that Madracis is a specialist coral, with colonies harboring a single symbiont from the genus Breviolum (formerly clade B). However, these previous studies have not precisely addressed if Madracis is colonized by several types of Symbiodiniaceae simultaneously or whether this coral is a specialist. The hypothesis that Madracis is a generalist coral host was evaluated in the present study. A total of 1.9 million reads of ITS2 nuclear ribosomal DNA were obtained by Illumina MiSeq sequencing. While Symbiodiniaceae ITS2 sequences between two sampling depths were almost entirely (62%) from the genus Breviolum (formerly clade B), shallow (10-15 m) populations in Abrolhos had a greater diversity of ITS2 sequences in comparison to deeper (25-35 m) populations of St. Peter and St. Paul Archipelago. Cladocopium (formerly clade C) and Symbiodinium (formerly clade A) were also found in Abrolhos. A single Madracis colony can host different symbiont types with > 30 Symbiodiniaceae ITS2-type profiles. Abrolhos corals presented a higher photosynthetic potential as a possible result of co-occurrence of multiple Symbiodiniaceae in a single coral colony. Multiple genera/clades of Symbiodiniaceae possibly confer coral hosts with broader environmental tolerance and ability to occupy diverse or changing habitats.

Inhibition of SARS-CoV-2 infection in human iPSC-derived cardiomyocytes by targeting the Sigma-1 receptor disrupts cytoarchitecture and beating.

SARS-CoV-2 infects cardiac cells and causes heart dysfunction. Conditions such as myocarditis and arrhythmia have been reported in COVID-19 patients. The Sigma-1 receptor (S1R) is a ubiquitously expressed chaperone that plays a central role in cardiomyocyte function. S1R has been proposed as a therapeutic target because it may affect SARS-CoV-2 replication; however, the impact of the inhibition of S1R in human cardiomyocytes remains to be described. In this study, we investigated the consequences of S1R inhibition in iPSC-derived human cardiomyocytes (hiPSC-CM). SARS-CoV-2 infection in hiPSC-CM was productive and reduced cell survival. S1R inhibition decreased both the number of infected cells and viral particles after 48 hours. S1R inhibition also prevented the release of pro-inflammatory cytokines and cell death. Although the S1R antagonist NE-100 triggered those protective effects, it compromised cytoskeleton integrity by downregulating the expression of structural-related genes and reducing beating frequency. Our findings suggest that the detrimental effects of S1R inhibition in human cardiomyocytes' integrity may abrogate its therapeutic potential against COVID and should be carefully considered.

A new genomic taxonomy system for the Synechococcus collective.

Cyanobacteria of the genus Synechococcus are major contributors to global primary productivity and are found in a wide range of aquatic ecosystems. This Synechococcus collective (SC) is metabolically diverse, with some lineages thriving in polar and nutrient-rich locations and others in tropical or riverine waters. Although many studies have discussed the ecology and evolution of the SC, there is a paucity of knowledge on its taxonomic structure. Thus, we present a new taxonomic classification framework for the SC based on recent advances in microbial genomic taxonomy. Phylogenomic analyses of 1085 cyanobacterial genomes demonstrate that organisms classified as Synechococcus are polyphyletic at the order rank. The SC is classified into 15 genera, which are placed into five distinct orders within the phylum Cyanobacteria: (i) Synechococcales (Cyanobium, Inmanicoccus, Lacustricoccus gen. Nov., Parasynechococcus, Pseudosynechococcus, Regnicoccus, Synechospongium gen. nov., Synechococcus and Vulcanococcus); (ii) Cyanobacteriales (Limnothrix); (iii) Leptococcales (Brevicoccus and Leptococcus); (iv) Thermosynechococcales (Stenotopis and Thermosynechococcus) and (v) Neosynechococcales (Neosynechococcus). The newly proposed classification is consistent with habitat distribution patterns (seawater, freshwater, brackish and thermal environments) and reflects the ecological and evolutionary relationships of the SC.

Unlocking the Genomic Taxonomy of the Prochlorococcus Collective.

Prochlorococcus is the most abundant photosynthetic prokaryote on our planet. The extensive ecological literature on the Prochlorococcus collective (PC) is based on the assumption that it comprises one single genus comprising the species Prochlorococcus marinus, containing itself a collective of ecotypes. Ecologists adopt the distributed genome hypothesis of an open pan-genome to explain the observed genomic diversity and evolution patterns of the ecotypes within PC. Novel genomic data for the PC prompted us to revisit this group, applying the current methods used in genomic taxonomy. As a result, we were able to distinguish the five genera: Prochlorococcus, Eurycolium, Prolificoccus, Thaumococcus, and Riococcus. The novel genera have distinct genomic and ecological attributes.