Engineering natural microbiomes for biotechnological applications remains challenging, as metabolic interactions within microbiomes are largely unknown, and practical principles and tools for microbiome engineering are still lacking. Here, we present a combinatory top-down and bottom-up framework to engineer natural microbiomes for the construction of function-enhanced synthetic microbiomes. We show that application of herbicide and herbicide-degrader inoculation drives a convergent succession of different natural microbiomes toward functional microbiomes (e.g., enhanced bioremediation of herbicide-contaminated soils). We develop a metabolic modeling pipeline, SuperCC, that can be used to document metabolic interactions within microbiomes and to simulate the performances of different microbiomes. Using SuperCC, we construct bioremediation-enhanced synthetic microbiomes based on 18 keystone species identified from natural microbiomes. Our results highlight the importance of metabolic interactions in shaping microbiome functions and provide practical guidance for engineering natural microbiomes.

A bacterial community was enriched with polycyclic aromatic hydrocarbons (PAHs) polluted soil to better study PAH degradation by indigenous soil bacteria. The consortium degraded more than 52% of low molecular weight and 35% of high molecular weight (HMW) PAHs during 16 days in a soil leachate medium. 16S rRNA gene high-throughput sequencing and quantitative polymerase chain reaction analyses for alpha subunit genes of ring-hydroxylating-dioxygenase (RHDα) suggested that Proteobacteria and Actinobacteria at the phylum level, Pseudomonas, Methylobacillus, Nocardioides, Methylophilaceae, Achromobacter, Pseudoxanthomonas, and Caulobacter at the generic level were involved in PAH degradation and might have the ability to carry RHDα genes (nidA and nahAc). The community was selected and collected according to biomass and RHDα gene contents, and added back to the PAH-polluted soil. The 16 EPA priority PAHs decreased from 95.23 to 23.41 mg kg-1 over 35 days. Compared with soil without the introduction of this bacterial community, adding the community with RHDα genes significantly decreased soil PAH contents, particularly HMW PAHs. The metabolic rate of PAHs in soil was positively correlated with nidA and nahAc gene contents. These results indicate that adding an indigenous bacterial consortium containing RHDα genes to contaminated soil may be a feasible and environmentally friendly method to clean up PAHs in agricultural soil.

Biochars are used globally in agricultural crop production and environmental remediation. However, environmentally persistent free radicals (EPFRs), which are stable emerging pollutants, are generated as a characteristic feature during biomass pyrolysis. EPFRs can induce the formation of reactive oxygen species, which poses huge agro-environmental and human health risks. Their half-lives and persistence in both biochar residues and in the atmosphere may lead to potentially adverse risks in the environment. This review highlights the comprehensive research into these bioreactive radicals, as well as the bottlenecks of biochar production leading up to the formation and persistence of EPFRs. Additionally, a way forward has been proposed, based on two main recommendations. A global joint initiative to create an all-encompassing regulations policy document that will improve both the technological and the quality control aspects of biochars to reduce EPFR generation at the production level. Furthermore, environmental impact and risk assessment studies should be conducted in the extensive applications of biochars in order to protect the environmental and human health. The highlighted key research directions proposed herein will shape the production, research, and adoption aspects of biochars, which will mitigate the considerable concerns raised on EPFRs.