Microbiome analysis of surface water of three sites with different anthropogenic contamination of the Rio de La Plata River, Argentina

BLANCO FERNÁNDEZ MD; ZAMBRANA MONTAÑO R; TORRES C

Workshop; CADDE Workshop on Portable Metagenomics for Pathogen Surveillance; 2023

The Río de la Plata River is the estuary of a vast basin in Buenos Aires, Argentina that leads to the Atlantic Ocean. It has a variable width, from 40 km at its upper to 230 km at its mouth. Along its course several cities and industries discharge their sewage and wastewater into the river. Also saline concentration rises as it becomes near the ocean. The aim of this work was to make a first approximation to the microbiome and DNA viromes of three points of this river : Punta Indio, La Balandra and Quilmes. Samples (20 liters) were filtered through 1, 0,45 and 0,22 μm pore filter and then concentrated using hollow-fiber ultrafiltration modules of 50 kDa. Samples were further concentrated using polietilenglicol precipitation and the totality of the DNA of the sample was extracted using phenol-chloroform, followed by ethanol precipitation and final purification using a commercial kit. DNA was sequenced using Illumina technology. Approximately, 40 million reads (150 pb) per metagenome were obtained and reads were trimmed and quality filtered using TrimGalore and de-novo assembled using Megahit, and metaSpades with different kmers configurations. Assemblies were assessed using QUAST and contigs larger than 1 kb were analyzed. Approximately 1.5 x 105 contigs per assembly were obtained and 4-7% were of viral origin. Metagenome-assembled-genomes (MAGs) were obtained using Metawrap pipeline with minor modifications. Abundance of virus and bacteria was calculated using kraken2 followed by Bracken. Viral contigs were further filtered using Virsorter2 followed by CheckV and VirHunter. Viromes were clearly dominated by Duplodnaviria realm and Caudoviricetes order (0.93-0.95) , followed by Varidnaviria (0.03-0.05) and unclassified viruses (0.01-0.03) meanwhile abundance of Monodnaviria with the presence of Parvoviridae and Papillomaviridae families were less than 0.007. Genomes of the Varidnaviridae domain belonged to the Phycodnaviridae and Chlorovirus and Prasinovirus genuses. Virus genomes classified as High Quality were annotated using Prodigal, Ugene and HHPred. 60 viral MAGs of high quality and 142 of medium quality were obtained. We are currently analyzing this genomes, performing analyses directed to virus discovery and detection of viral – host relationship.