Pathogens in soil play a tremendous role in soil health and subsequent food production. Soil-borne pathogens can cause serious losses to global harvest and are considered as a difficult problem to manage worldwide. The emergence of soil disease is largely dependent on the pathogen-host-environment complex, which can be employed to generate pathogen control strategies. Usually, the resources of resistant plant varieties are limited, and chemical control is insufficiently effective with possible secondary soil pollution. Therefore, there is now a compulsory need to enhance the ability of soil per se to defend against invading pathogens (i.e. soil immunity). Soil immunity is normally attributed to the activities of the functional microbiome. In the meanwhile, pathogen-microbiome interactions in soil are sensitive to soil contaminants which would filter out unique groups of microbial communities. Steering functional soil microbiome will not only limit disease development, but also reduce the level of soil pollution. It is thus of great importance to develop microbiome-based techniques to improve soil immunity and resilience. This review provided an up-to-date understanding of the mechanisms for microbiome-based disease suppression and potential management strategies for better sustainable agricultural system.

The Green Revolution of the mid-20th century transformed agriculture worldwide and has resulted in environmental challenges. A new approach, the Second Green Revolution, seeks to enhance agricultural productivity while minimizing negative environmental impacts. Plant microbiomes play critical roles in plant growth and stress responses, and understanding plant-microbiome interactions is essential for developing sustainable agricultural practices that meet food security and safety challenges, which are among the United Nations Sustainable Development Goals. This review provides a comprehensive exploration of key deterministic processes crucial for developing microbiome management strategies, including the host effect, the facilitator effect, and microbe-microbe interactions. A hierarchical framework for plant microbiome modulation is proposed to bridge the gap between basic research and agricultural applications. This framework emphasizes three levels of modulation: single-strain, synthetic community, and in situ microbiome modulation. Overall, rational management of plant microbiomes has wide-ranging applications in agriculture and can potentially be a core technology for the Second Green Revolution.

Research is establishing a systems biology view of biological response to Cd stress. It is meaningful to explore whether there is regulatory isomorphy among distantly related organisms.

Aerobic composting is a key strategy to the sustainable use of livestock manure, which is however constrained by the slow kinetics. Microbe-aided thermophilic composting provides an attractive solution to this problem. In this study, we identified key thermophilic bacteria capable of accelerating manure composting based on the deciphering of manure bacterial community evolution in a thermophilic system. High-throughput sequencing showed a significant evolution of manure bacterial community structure with the increasing heating temperature. Firmicutes were substantially enriched by the heating, particularly some known thermotolerant bacterial species, such as Novibacillus thermophiles, Bacillus thermolactis, and Ammoniibacillus agariperforans. Correspondingly, through function prediction, we found bacterial taxa with cellulolytic and xylanolytic activities were significantly higher in the thermophilic process relative to the initial stage. Subsequently, a total of 47 bacteria were isolated in situ and their phylogenetic affiliation and degradation capacity were determined. Three isolates were back inoculated to the manure, resulting in shortened composting process from 5 to 3 days with Germination Index increased up to 134%, and improved compost quality particularly in wheat growth promoting. Comparing to the mesophilic and thermophilic Bacillus, the genomes of the three isolates manifested some features similar to the thermophiles, including smaller genome size and mutation of specific genes that enhance heat tolerance. This study provide robust evidence that microbe-aided thermophilic composting is capable to accelerate manure composting and improve the quality of compost, which represents a new hope to the sustainable use of manure from the meat industry.

Functional metagenomics is a premise-free approach for exploring metal resistance genes, enabling more profound effects on the development of bioremediation tools than pure culture based selection. Six soil metagenomic libraries were screened for copper (Cu) resistance genes in the current study through conventional functional genomics. Clones from the six metagenomic libraries were randomly selected from solid medium supplied with Cu, resulting in 411 Cu resistance clones. Thirty-five clones with the strongest Cu resistance were sequenced and 12 unique sequences harboring 25 putative open reading frames were obtained. It is inferred by bioinformatic analysis that putative genes carried by these recombinant plasmids probably function in the pathways of responding to Cu stress, including energy metabolism, integral components of membrane, ion transport/chelation, protein/amino acid metabolism, carbohydrate/fatty acid metabolism, signal transduction and DNA binding. The sequenced clones were re-transformed into Escherichia coli strain DH5α, and the host's biomass and the metal sorption under Cu stress were subsequently determined. The results showed that the biomass of eight of the clones was significantly increased, whereas four of them were significantly reduced. A negative correlation (R = 0.86) was found between the biomass and Cu sorption capacity. The 12 positive clones were further transferred into a Cu-sensitive E. coli strain (ΔCopA), among which nine restored the host's Cu resistance substantially. The Cu resistant genes explored in this study by functional metagenomics possess a potential capacity for developing novel bioremediation strategies, and the findings imply a vast diversity of microbial Cu resistance genetic factors in soil yet to be discovered.

Editorial: Highlighting the Role of Microbes in Greener Wastewater Treatment