Significant progress has been made in understanding microbial roles in agriculture and environmental systems. Studies revealing the diversity and host associations of tick microbiomes, the enhancement of microalgal and plant growth through optimizing trace metals and bioemulsifiers, and microbial consortia’s contribution to biodegradation of pollutants exemplify this trend. Novel findings also uncover the complex microbiomes within tree woody tissues and fermentation microbiota shaping food flavor and functional properties, offering insight into sustainable resource management and ecological health.