Fan Lü

Bioaugmentation is an environmentally friendly technique for alleviating the ammonium inhibition in anaerobic digestion (AD). However, it is challenging to establish an effective bioaugmentation agent. In this study, a consortium was constructed, comprising the multi-functional bacterium Coprothermobacter proteolyticus and the hydrogenotrophic methanogen Methanothermobacter thermautotrophicus, and validated its bioaugmentation performance in semi-continuous thermophilic digester under varying ammonium stresses. The results indicated that, under stressful environment of 4 g NH4+-N/L, the addition of this consortium restored the methanogenic performance of AD system to 87.7% of its pre-ammonium shock level and maintained system robustness over the subsequent 50 days of operation. Metagenomic analyses indicated that the addition of this consortium disrupted the inhibitory steady state of the anaerobic microbial ecosystems, stimulated the enrichment of another robust symbiotic consortium comprising Methanothermobacter and Syntrophaceticus species, and drive additional microbial species to coordinate the methanogenesis process. Genome-centric metatranscriptomic analyses provides new insights into the mechanism of action of Coprothermobacter proteolyticus. Coprothermobacter proteolyticus can form microbial aggregates with other microorganisms, and promotes the survival of Methanothermobacter and Syntrophaceticus species by mediating direct interspecies electron transfer and horizontal gene transfer via cytochrome C and Type IV pilus, beyond producing acetic acid, CO2, and H2 to provide substrate for methanogenesis. Methanothermobacter thermautotrophicus resulted in an initial reduction in hydrogen partial pressure, thereby promoting the growth of indigenous species of Methanothermobacter and Syntrophaceticus. Consequently, the simultaneous introduction of Coprothermobacter proteolyticus and Methanothermobacter thermautotrophicus likely functions across multiple metabolic pathways, thereby facilitating the rapid adaptation of the AD system to stressful environment of 4 g NH4+-N/L.

Temperature influences microbial metabolic activity, which is crucial for biotechnological processes and bioproducts stabilization. However, temperature-driven responses of complex viruses and prokaryotic communities, and the modulatory role of viruses in prokaryotic community within environmental biotechnology systems, remain poorly understood. We developed a continuous thermal stress system with temperature gradients and high-resolution temporal sampling of metagenomics and metatranscriptomics, using municipal organic solid waste as a biological model. An optimized meta-omics pipeline integrating genomic potential and activity was applied to investigate the adaptive dynamics of complex prokaryotic and viral communities. Continuous thermal stress triggered stress responses in paired virus-hosts within the system. Thermal stress exerted distinct effects on temperate and virulent viruses. Viruses formed quasi-symbiotic alliances with their hosts to withstand thermal stress by integrating protein folding genes, stress response, and metabolic function genes, shaping host adaptability under thermal pressure. Equipped with multiple defense and counter-defense systems, viruses accelerated the accumulation of beneficial mutations under thermal stress, enabling them to escape host immunity and intensify competition with prokaryotic communities. This study demonstrates how viruses accelerated both the restructuring and adaptive responses of prokaryotic communities under thermal stress, advancing our understanding of phage-based therapeutic strategies in temperature-variable engineering applications.