Metagenomics Combined with Stable Isotope Probe (SIP) for the Discovery of Novel Dehalogenases Producing Bacteria

Macroalgal microbiomes unveil a valuable genetic resource for halogen metabolism

BACKGROUND

Macroalgae, especially reds (Rhodophyta Division) and browns (Phaeophyta Division), are known for producing various halogenated compounds. Yet, the reasons underlying their production and the fate of these metabolites remain largely unknown. Some theories suggest their potential antimicrobial activity and involvement in interactions between macroalgae and prokaryotes. However, detailed investigations are currently missing on how the genetic information of prokaryotic communities associated with macroalgae may influence the fate of organohalogenated molecules.

RESULTS

To address this challenge, we created a specialized dataset containing 161 enzymes, each with a complete enzyme commission number, known to be involved in halogen metabolism. This dataset served as a reference to annotate the corresponding genes encoded in both the metagenomic contigs and 98 metagenome-assembled genomes (MAGs) obtained from the microbiome of 2 red (Sphaerococcus coronopifolius and Asparagopsis taxiformis) and 1 brown (Halopteris scoparia) macroalgae. We detected many dehalogenation-related genes, particularly those with hydrolytic functions, suggesting their potential involvement in the degradation of a wide spectrum of halocarbons and haloaromatic molecules, including anthropogenic compounds. We uncovered an array of degradative gene functions within MAGs, spanning various bacterial orders such as Rhodobacterales, Rhizobiales, Caulobacterales, Geminicoccales, Sphingomonadales, Granulosicoccales, Microtrichales, and Pseudomonadales. Less abundant than degradative functions, we also uncovered genes associated with the biosynthesis of halogenated antimicrobial compounds and metabolites.

CONCLUSION

The functional data provided here contribute to understanding the still largely unexplored role of unknown prokaryotes. These findings support the hypothesis that macroalgae function as holobionts, where the metabolism of halogenated compounds might play a role in symbiogenesis and act as a possible defense mechanism against environmental chemical stressors. Furthermore, bacterial groups, previously never connected with organohalogen metabolism, e.g., Caulobacterales, Geminicoccales, Granulosicoccales, and Microtrichales, functionally characterized through MAGs reconstruction, revealed a biotechnologically relevant gene content, useful in synthetic biology, and bioprospecting applications. Video Abstract.

Short Peptides for Hydrolase Supramolecular Mimicry and Their Potential Applications

Hydrolases are enzymes that have found numerous applications in various industrial sectors spanning from pharmaceuticals to foodstuff and beverages, consumers' products such as detergents and personal care, textiles, and even for biodiesel production and environmental bioremediation. Self-assembling and gelling short peptides have been designed for their mimicry so that their supramolecular organization leads to the creation of hydrophobic pockets for catalysis to occur. Catalytic gels of this kind can also find numerous industrial applications to address important global challenges of our time. This concise review focuses on the last 5 years of progress in this fast-paced, popular field of research with an eye towards the future.

Impact of PVC microplastics on soil chemical and microbiological parameters

Microplastics (MPs) are emerging pollutants whose occurrence is a global problem in natural ecosystems including soil. Among MPs, polyvinyl chloride (PVC) is a well-known polymer with remarkable resistance to degradation, and because its recalcitrant nature serious environmental concerns are created during manufacturing and waste disposal. The effect of PVC (0.021% w/w) on chemical and microbial parameters of an agricultural soil was tested by a microcosm experiment at different incubation times (from 3 to 360 days). Among chemical parameters, soil CO₂ emission, fluorescein diacetate (FDA) activity, total organic C (TOC), total N, water extractable organic C (WEOC), water extractable N (WEN) and SUVA₂₅₄ were considered, while the structure of soil microbial communities was studied at different taxonomic levels (phylum and genus) by sequencing bacterial 16S and fungal ITS2 rDNA (Illumina MiSeq). Although some fluctuations were found, chemical and microbiological parameters exhibited some significant trends. Significant (p < 0.05) variations of soil CO₂ emission, FDA hydrolysis, TOC, WEOC and WEN were found in PVC-treated soils over different incubation times. Considering the structure of soil microbial communities, the presence of PVC significantly (p < 0.05) affected the abundances of specific bacterial and fungal taxa: Candidatus_Saccharibacteria, Proteobacteria, Actinobacteria, Acidobacteria and Bacteroides among bacteria, and Basidiomycota, Mortierellomycota and Ascomycota among fungi. After one year of experiment, a reduction of the number and the dimensions of PVC was detected supposing a possible role of microorganisms on PVC degradation. The abundance of both bacterial and fungal taxa at phylum and genus level was also affected by PVC, suggesting that the impact of this polymer could be taxa-dependent.