Inter-phylum negative interactions affect soil bacterial community dynamics and functions during soybean development under long-term nitrogen fertilization

Fertilization treatments affect soil CO2 emission through regulating soil bacterial community composition in the semiarid Loess Plateau

A growing body of literature have emphasized the effects of fertilization regimes on soil respiration and microbial community in the semiarid region, however, fertilization treatment effects on the soil CO2 emission, soil bacterial community, and their relationships from long-term experiments is lacking. In the present study, we investigated the effects of long-term fertilization regimes on soil bacterial community and thereafter on soil CO2 emission. A 9-year field experiment was conducted with five treatments, including no fertilizer (NA) and four fertilization treatments (inorganic fertilizer (CF), inorganic plus organic fertilizer (SC), organic fertilizer (SM), and maize straw (MS)) with equal N input as N 200 kg hm-2. The results indicated that CO2 emission was significantly increased under fertilization treatments compared to NA treatment. The bacterial abundance was higher under MS treatment than under NA treatment, while the Chao1 richness showed opposite trend. MS treatment significantly change soil bacterial community composition compared to NA treatment, the phyla (Alphaproteobacteria and Gammaproteobacteria) and potential keystone taxa (Nitrosomonadaceae and Beijerinckiaceae) were higher, while the Acidobacteriota was lower under MS treatment than under NA treatment. CO2 emission was positively correlated with the abundance of Alphaproteobacteria, Gammaproteobacteria, and keystone taxa, negatively correlated with these of Acidobacteriota. Random forest modeling and structural equation modeling determined soil organic carbon, total nitrogen, and the composition and network module III of the bacterial community are the main factors contribute to CO2 emission. In conclusion, our results suggest that the increased CO2 emission was affected by the varied of soil bacterial community composition derived from fertilization treatments, which was related to Alphaproteobacteria, Gammaproteobacteria, Acidobacteriota, and potential keystone taxa (Nitrosomonadaceae and Beijerinckiaceae), and highlight that the ecological importance of the bacterial community in mediating carbon cycling in the semiarid Loess Plateau.

Whole-plant microbiome profiling reveals a novel geminivirus associated with soybean stay-green disease

Microbiota colonize every accessible plant tissue and play fundamental roles in plant growth and health. Soybean stay-green syndrome (SGS), a condition that causes delayed leaf senescence (stay-green), flat pods and abnormal seeds of soybean, has become the most serious disease of soybean in China. However, the direct cause of SGS is highly debated, and little is known about how SGS affect soybean microbiome dynamics, particularly the seed microbiome. We studied the bacterial, fungal, and viral communities associated with different soybean tissues with and without SGS using a multi-omics approach, and investigated the possible pathogenic agents associated with SGS and how SGS affects the assembly and functions of plant-associated microbiomes. We obtained a comprehensive view of the composition, function, loads, diversity, and dynamics of soybean microbiomes in the rhizosphere, root, stem, leaf, pod, and seed compartments, and discovered that soybean SGS was associated with dramatically increased microbial loads and dysbiosis of the bacterial microbiota in seeds. Furthermore, we identified a novel geminivirus that was strongly associated with soybean SGS, regardless of plant cultivar, sampling location, or harvest year. This whole-plant microbiome profiling of soybean provides the first demonstration of geminivirus infection associated with microbiota dysbiosis, which might represent a general microbiological symptom of plant diseases.

Linking soil fungi to bacterial community assembly in arid ecosystems

Revealing the roles of biotic factors in driving community assembly, which is crucial for the understanding of biodiversity and ecosystem functions, is a fundamental but infrequently investigated subject in microbial ecology. Here, combining a cross-biome observational study with an experimental microcosm study, we provided evidence to reveal the major roles of biotic factors (i.e., soil fungi and cross-kingdom species associations) in determining soil bacterial biogeography and community assembly in complex terrestrial ecosystems of the arid regions of northwest China. The results showed that the soil fungal richness mediates the balance of assembly processes of bacterial communities, and stochastic assembly processes decreased with increasing fungal richness. Our results further suggest that the predicted increase in aridity conditions due to climate change will reduce bacterial α-diversity, particularly in desert soils and subsurface layer, and induce more negative species associations. Together, our study represents a significant advance in linking soil fungi to the mechanisms underlying bacterial biogeographic patterns and community assembly in arid ecosystems under climate aridity and land-use change scenarios.