The Raphidiopsis (= Cylindrospermopsis) raciborskii pangenome updated: Two new metagenome-assembled genomes from the South American clade.

Two Raphidiopsis (=Cylindrospermopsis) raciborskii metagenome-assembled genomes (MAGs) were recovered from two freshwater metagenomic datasets sampled in 2011 and 2012 in Pampulha Lake, a hypereutrophic, artificial, shallow reservoir, located in the city of Belo Horizonte (MG), Brazil. Since the late 1970s, the lake has undergone increasing eutrophication pressure, due to wastewater input, leading to the occurrence of frequent cyanobacterial blooms. The major difference observed between PAMP2011 and PAMP2012 MAGs was the lack of the saxitoxin gene cluster in PAMP2012, which also presented a smaller genome, while PAMP2011 presented the complete sxt cluster and all essential proteins and clusters. The pangenome analysis was performed with all Raphidiopsis/Cylindrospermopsis genomes available at NCBI to date, with the addition of PAMP2011 and PAMP2012 MAGs (All33 subset), but also without the South American strains (noSA subset), and only among the South American strains (SA10 and SA8 subsets). We observed a substantial increase in the core genome size for the 'noSA' subset, in comparison to 'All33' subset, and since the core genome reflects the closeness among the pangenome members, the results strongly suggest that the conservation level of the essential gene repertoire seems to be affected by the geographic origin of the strains being analyzed, supporting the existence of a distinct SA clade. The Raphidiopsis pangenome comprised a total of 7943 orthologous protein clusters, and the two new MAGs increased the pangenome size by 11%. The pangenome based phylogenetic relationships among the 33 analyzed genomes showed that the SA genomes clustered together with 99% bootstrap support, reinforcing the metabolic particularity of the Raphidiopsis South American clade, related to its saxitoxin producing unique ability, while also indicating a different evolutionary history due to its geographic isolation.

Diversity assessment of photosynthesizers: comparative analysis of pre-cultivated and natural microbiome of sediments from Cerrado biome in Maranhão, Brazil.

Photosynthetic microorganisms are important components of most ecosystems and have important roles regarding biogeochemical cycles and the basis of the trophic chain. However, they sometimes are present in low abundance compared to other heterotrophic organisms. The Chapada das Mesas National Park (PNCM) is a Conservation Unit in Brazilian Cerrado biome, which is considered a hotspot for biodiversity conservation and possesses important rivers, waterfalls, and springs with economical and touristic importance. The aim of this study was to perform a comparative analysis of enriched and total microbiome of sediments to understand the impact of pre-cultivation in discovery of underrepresented groups like photosynthesizers. All sediment samples were cultivated in BG-11 medium under illumination to enrich for photosynthetic microorganisms and both the raw samples and the enriched ones were submitted to DNA extraction and sequencing of the V3-V4 hypervariable region of the 16S rRNA gene on the Ion Torrent platform. The reads were analyzed using QIIME2 software and the Phyloseq package. The enrichment allowed detection and identification of many genera of cyanobacteria in the Chapada das Mesas National Park (PNCM), which would probably not be possible without the combination of approaches. A total of 58 groups of photosynthetic microorganisms were classified in the samples from the enrichments and their relative abundance based on amplified 16S rRNA sequences were estimated, highlighting the genus Synechocystis which represented 10.10% of the abundance of the phylum Cyanobacteria and the genus Dunaliella, which represented 45.66% of the abundance of algae as the most abundant groups at the PNCM. In the enrichments, microorganisms from the phyla Proteobacteria (45.2%), Bacteroidetes (18%), and Planctomycetes (3.3%) were also identified, since there are ecological associations between the photosynthetic community and other groups of heterotrophic microorganisms. As for the functional analysis, metabolic functions associated with methanotrophy and methylotrophy, hydrocarbon degradation, phototrophy, and nitrogen fixation were predicted. The results highlight a great diversity of photosynthetic microorganisms in Cerrado and the importance of using a combination of approaches when analyzing target groups which are usually underrepresented such as cyanobacteria and microalgae.

vHULK, a New Tool for Bacteriophage Host Prediction Based on Annotated Genomic Features and Neural Networks.

Background: The experimental determination of a bacteriophage host is a laborious procedure. Thus, there is a pressing need for reliable computational predictions of bacteriophage hosts. Materials and Methods: We developed the program vHULK for phage host prediction based on 9504 phage genome features, which consider alignment significance scores between predicted proteins and a curated database of viral protein families. The features were fed to a neural network, and two models were trained to predict 77 host genera and 118 host species. Results: In controlled random test sets with 90% redundancy reduction in terms of protein similarity, vHULK obtained on average 83% precision and 79% recall at the genus level, and 71% precision and 67% recall at the species level. The performance of vHULK was compared against three other tools on a test data set with 2153 phage genomes. On this data set, vHULK achieved better performance at both the genus and the species levels than the other tools. Conclusions: Our results suggest that vHULK represents an advance on the state of art in phage host prediction.

Genomic Characterization of mcr-1.1-Producing Escherichia coli Recovered From Human Infections in São Paulo, Brazil.

Polymyxins are one of most important antibiotics available for multidrug-resistant Gram-negative infections. Diverse chromosomal resistance mechanisms have been described, but the polymyxin resistance phenotype is not yet completely understood. The objective of this study was to characterize colistin resistant mcr-1-producing strains isolated from human infections over one year in a hospital setting (Hospital das Clínicas, São Paulo, Brazil). We isolated 490 colistin-resistant Gram-negative rods, of which eight were mcr-1.1-positive Escherichia coli, the only species with this result, indicating a low incidence of the mcr-1 production mechanism among colistin-resistant isolates. All mcr-1.1 positive isolates showed similarly low MICs for colistin and were susceptible to most antibiotics tested. The isolates showed diversity of MLST classification. The eight mcr-1.1-positive E. coli genomes were sequenced. In seven of eight isolates the mcr-1.1 gene is located in a contig that is presumed to be a part of an IncX4 plasmid; in one isolate, it is located in a contig that is presumed to be part of an IncHI2A plasmid. Three different genomic contexts for mcr-1.1 were observed, including a genomic cassette mcr-1.1-pap2 disrupting a DUF2806 domain-containing gene in six isolates. In addition, an IS1-family transposase was found inserted next to the mcr-1.1 cassette in one isolate. An mcr-1.1-pap2 genomic cassette not disrupting any gene was identified in another isolate. Our results suggest that plasmid dissemination of hospital-resident strains took place during the study period and highlight the need for continued genomic surveillance.

High-quality draft genome sequence of pantanalinema sp. GBBB05, a cyanobacterium from cerrado biome

Cyanobacteria comprise one of the oldest and most diverse phyla in the Bacteria domain and are recognized for their importance in the biosphere evolution. Members of this phylum can be found in a wide variety of environments reflecting their photosynthetic ability, adaptability to various environmental conditions, and diversified metabolism. Such characteristics make cyanobacteria one of the preferred targets for research on bioactive compounds and new enzymes (Schirrmeister et al., 2011; Dittmann et al., 2015). Pantanalinema was described as a new genus of the Leptolyngbyaceae cyanobacterial family by a polyphasic approach, which included morphological characteristics, 16S rRNA gene phylogeny, 16S-23S ITS rRNA secondary structures, and physiological characteristics such as adaptability to pH variations (Vaz et al., 2015). This genus has been described only in Brazilian biomes such as the Pantanal and the Amazon, the first isolates being found in a lake. These Pantanalinema isolates were characterized by their ability to grow over a wide pH range (pH 4 to 11) as well as to modify the culture medium pH around neutrality (pH 6 to 7.4). Due to these characteristics, it is thought that this genus can occupy a variety of ecological niches, such as alkaline or slightly acidic water bodies (Vaz et al., 2015; Genuário et al., 2017). Taxonomic classification of Pantanalinema isolates requires the use of molecular markers as this genus is morphologically very similar to the recently described genus Amazoninema, which, in turn, has comparable morphology to other genera of the Leptolyngbyaceae family (Genuário et al., 2018). In this work, we report the genome sequence of a new Pantanalinema strain, named GBBB05, which was isolated from the Brazilian Cerrado biome. This is the first genome assembly for the Pantanalinema genus, which, along with the analyses provided here, is expected to enhance our understanding of this genus’s metabolic potential