The Marmib project aims to investigate the impact of microplastics on the spread of antimicrobial resistant bacteria in marine environment. This year, two postdocs have joined the project - one located in Tromsø (Feb 2022) and one located in Oslo (Mar 2022). The project design includes incubation of known microplastic polymers worldwide for standardization of DNA extraction and metal analysis in the sourrounding water. We carried out the first incubation testing using a novel incubation device invented at NORCE. We have tested different extraction methods and different polymers and finalized a method and polymers to use worldwide. The implantation has been delayed due to stainless steel shortage caused by the war in Ukraine. We have managed to secure steel from Germany and four out of five devices are now ready to ship to our partners which are Costa Rica, Vietnam, South African, Germany. The last one is going to ship to Estonia last since this country can only deploy the device during warmer period.
In addition, we have been developing "metagenomix" (https://github.com/FranckLejzerowicz/metagenomix), a modular and versatile tool to create, manage, monitor, and export shotgun metagenomics analysis results, for (currently) ca. 60 softwares which can all be fully configured to allow traceability, reproducibility, and benchmarking. It relies of an ecosystem of softwares tailored for high-performance computing (HPC), and currently being tested on the Sigma2 national e-infrastructure SAGA. We notably installed the Web of Life and Genome Taxonomy databases, as well as metagenome-assembled genome (MAG) collections (e.g., Tara Oceans: prokaryotic and eukaryotic). For these reference sequences, we built indices so that every user of the Norwegian Research Infrastructure Services (NRIS) can efficiently map reads using various aligners to obtain meaningful taxonomic, functional, and genomic classifications. These resources are harnessed by five collaborators with limited HPC knowledge, including three students and four direct contributions to MarMip. Notably, we initiated a meta-analysis of 144 publicly available metagenomes to reconstruct microplastic-associated MAGs, in the absence of cross-cutting metadata. Analyses. For this and three other MarMip datasets designed to understand the (1) resistome eco-evolution in lakes and wastewaters, (ii) impact of microplastics-antibiotics treatments on sediment and compost used as manure, and (iii) mobilization of ARGs in Costa Rica waters and sediments, we used over 150k CPU hours. Indeed, these projects collectively represent of volume of ca. 1.2 TB of raw data, that we aligned to various databases for taxonomic and functional classification, as well as assembled and binned for chromosome and plasmid characterization. Currently, we are completing the bioinformatic processing with mapping samples' reads onto assembled and annotated genomes, to perform the statistical analyses necessary to test for resistome and mobilome composition change across environments, host genomes and in response to microplastic addition. Despite the time zone difference, we frequently have digital meetings to discuss the progress of the project with partners.
Microplastics (MP) are already recognised as environmental pollutants of increasing concern. Ubiquitous, easily dispersed and extremely abundant, MP may be one of the defining features of the Anthropocene. Antimicrobial resistance genes (AMRGs), as well as antimicrobial products, heavy metals and resistant bacteria, have also been classified as types of pollution. Recently, evidence has been accumulating which indicates that these pollutants may be acting in tandem, worsening and driving another major problem facing the world today: antimicrobial resistance. MP provide not only a surface for biofilm formation (known as the plastisphere), they also enhance horizontal gene transfer and provide a physical vessel for spreading such resistance genes between different marine environments. Studies up to now have laid this foundation, but an investigation of the AMRGs present in plastisphere communities in different marine environments and dispersed by MPs is not done. We propose to fill this knowledge gap by studying the AMRGs, especially those present on plasmids (which are transferred between bacteria more readily), of MP collected from marine and close to marine environments from Vietnam, Norway, Baltic sea (Germany/Estonia), Costa Riva and South Africa. In the first phase of the project, we plan to collect and identifying MP, sequence microbiomes and compare levels of antibiotics/metals in the waters across different environments and levels of human interaction. This will inform the second phase of the project, in which AMRGs and bacteria present in the MP communities will be determined using metagenomic approaches. We will also characterise the plasmids from the plastisphere bacteria and how ecological functions in the marine may be changed due to biofilms being transported by the ocean to new locations. Finally, we will be to interact with policymakers and address the general public in advice on generating the next steps to address the problem of plastic waste.