Engineering a microbiosphere to clean up the ocean – inspiration from the plastisphere

Plastic is a ubiquitous material that has become an essential part of our lives. More than one hundred million tons of plastic has accumulated in the world’s oceans as a result of poor waste management. This plastic waste gradually fragments into smaller pieces known as microplastics and nanoplastics. These small plastic particles can cause significant damage to marine ecosystems, and negatively impact human health. According to a recent review of international patents, the majority of ocean-cleaning inventions are limited to microplastics larger than 20 μm. Furthermore, such technologies are ineffective for nanoplastics, which measure less than 1000 nm, or even fibrous plastics. Alternative solutions need to be considered for the large-scale in situ removal of microplastics and nanoplastics from the ocean. In this perspective, we present the concept of engineering a microbial ecosystem, which we term the microbiosphere. The concept is based on key observations that have been made for natural plastic-based ecosystems known as plastispheres. These observations relate to the solid support material, self-sustainability, attachment to plastic, degradation of plastic, and risk of pathogenicity. Inspiration can be taken from the plastisphere whereby a novel microbial ecosystem could be designed and engineered as a bioremediation tool to rid the ocean of micro- and nanoplastics. Such an engineered system could outcompete pathogens for marine plastic waste and potentially reduce the risk of infectious diseases

Complete genome sequence of Vibrio gazogenes PB1: an estuarine bacterium capable of producing prodigiosin from starch or cellulose

Vibrio is a genus of gram-negative, rod-shaped, motile bacteria commonly found in saltwater. One species in particular, Vibrio gazogenes PB1, sourced from an estuarine environment, is known to produce the secondary metabolite, prodigiosin. This high-value compound has potential uses as an antibiotic, a fungicide, and an anti-cancer agent. To further explore its metabolic and genetic features for biotechnological purposes, the complete genome sequence of V. gazogenes PB1 was determined by Illumina and Pacbio sequencing. Two chromosomes were assembled with a mean coverage of 293x. Chromosome 1 is 3.5 Mbp in size with 45.3% GC content and chromosome 2 is 1.2 Mbp in size with 45.1% GC content. The entire genome harbours 4178 genes, of which 3988 are protein-coding and 114 are RNA-coding. A total of 55 virulence-related genes, 38 antimicrobial resistance genes, 48 transposase sequences, 2 intact prophage regions, and 10 genomic islands were present within the genome. Six genes associated with the degradation of cellulose and starch were also identified within the genome. Four of them were strongly up-regulated, as confirmed by RT-qPCR, thus providing strong evidence for their involvement in starch and cellulose degradation. Quite importantly, we demonstrate for the first time that starch and cellulose is associated with the synthesis of prodigiosin in a native prodigiosin-producing bacterium. The prodigiosin titres obtained in the presence of cellulose were on par with glucose as the carbon source which lends further support in the use of V. gazogenes PB1 as a biotechnological host for prodigiosin production

The H-index is an unreliable research metric for evaluating the publication impact of experimental scientists

Research metrics are often used to assess the reputation of scientists. One commonly employed research metric is the H-index. It measures the publication impact of scientists. But how is it conceivable for a scientist with no distinguished track record in an experimental field to generate greater publication impact than prize-winning scientists? The answer, by resorting to a publishing strategy which places less focus on experimental innovations. I make the case here that the H-index is an abysmal metric for evaluating experimental researchers and that an alternative experiment-oriented metric is sorely needed to quantitate the work of experimental scientists