Soil metabolomics and bacterial functional traits revealed the responses of rhizosphere soil bacterial community to long-term continuous cropping of Tibetan barley

Abstract

Continuous cropping often leads to an unbalanced soil microbial community, which in turn negatively affects soil functions. However, systematic research of how these effects impact the bacterial composition, microbial functional traits, and soil metabolites is lacking. In the present study, the rhizosphere soil samples of Tibetan barley continuously monocropped for 2 (CCY02), 5 (CCY05), and 10 (CCY10) years were collected. By utilizing 16S high-throughput sequencing, untargeted metabolomes, and quantitative microbial element cycling smart chips, we examined the bacterial community structure, soil metabolites, and bacterial functional gene abundances, respectively. We found that bacterial richness (based on Chao1 and Phylogenetic Diversity [PD] indices) was significantly higher in CCY02 and CCY10 than in CCY05. As per principal component analysis (PCA), samples from the continuous monocropping year tended to share more similar species compositions and soil metabolites, and exhibited distinct patterns over time. The results of the Procrustes analysis indicated that alterations in the soil metabolic profiles and bacterial functional genes after long-term continuous cropping were mainly mediated by soil microbial communities (P < 0.05). Moreover, 14 genera mainly contributed to the sample dissimilarities. Of these, five genera were identified as the dominant shared taxa, including Blastococcus, Nocardioides, Sphingomonas, Bacillus, and Solirubrobacter. The continuous cropping of Tibetan barley significantly increased the abundances of genes related to C-degradation (F = 9.25, P = 0.01) and P-cycling (F = 5.35, P = 0.03). N-cycling significantly negatively correlated with bacterial diversity (r = − 0.71, P = 0.01). The co-occurrence network analysis revealed that nine hub genera correlated with most of the functional genes and a hub taxon, Desulfuromonadales, mainly co-occurred with the metabolites via both negative and positive correlations. Collectively, our findings indicated that continuous cropping significantly altered the bacterial community structure, functioning of rhizosphere soils, and soil metabolites, thereby providing a comprehensive understanding of the effects of the long-term continuous cropping of Tibetan barley.

Altering environmental conditions induce shifts in simulated deep terrestrial subsurface bacterial communities—Secretion of primary and secondary metabolites

“…Furthermore, tRNA constituent secretion (2‐thiocytidine dihydrate, hypoxanthine) was stimulated under most conditions in DD. Similar changes in the up‐ and down‐regulation of primary and secondary metabolite production in connection with environmental stress, have been previously reported for soil microbiota (Zhao et al, 2022). Phytohormones (e.g., IAA and gibberellins) are known to promote plant growth and to protect plants from salt stress in soils.…”

“…Altogether, microorganisms produce thousands of chemicals vital for life. For example, in soil samples from an alpine Tibetan barley experiment site, a total of 126 microbial metabolites were found to respond to the environmental stress caused by continuous cropping, including lipids, lipid-like molecules, organic acids and their derivatives, organoheterocyclic compounds, nucleosides, nucleotides as well as alkaloids and their derivatives (Zhao et al, 2022). Furthermore, amino acids are metabolised, synthesised, taken up and excreted by a large number of microorganisms.…”

Maize and peanut intercropping improves the nitrogen accumulation and yield per plant of maize by promoting the secretion of flavonoids and abundance of Bradyrhizobium in rhizosphere

“…Root exudates are important factors that affect the rhizosphere microbial communities ( Wang et al, 2022 ).To further clarify our second aim the relationship between flavonoids root exudates and soil bacterial community composition in intercropping systems, spearman’s correlation analysis revealed significant correlations between specific root exudates and bacterial community composition. Among these, cyanidin 3-sambubioside 5-glucosideand cyanidin 3-O-(6-Op-coumaroyl) glucoside-5-O-glucoside; shisonin had frequent significantly positive correlations with bacterial communities; the greatest correlation was with Bradyrhizobium ( Figure 6A and Supplementary Table S6 ), indicating that some root exudates secreted by the root changed the bacterial community composition, while, some bacterial metabolic pathways also changed to adapt to environmental stress ( Zhao et al, 2022b ). These results showed that root exudates could be used to assess the adaptations of soil microbial communities to interspecific interactions at the molecular level.…”

Effect of continuous planting on Casuarina equisetifolia rhizosphere soil physicochemical indexes, microbial functional diversity and metabolites

“…Continuous planting imbalances soil microbial communities, alters the function of soil microbes, disturbs nutrient cycling in the soil, and, in turn, affects plant growth ( Zhao et al., 2022 ). As BIOLOG ECO results ( Figure 1A ) showed, in the C. equisetifolia rhizosphere soil, the number of microorganisms utilizing phenolic acid, carboxylic acid, fatty acid, and amines as a carbon source significantly increases with the rise of continuous planting.…”