Metagenomic and machine learning-aided identification of biomarkers driving distinctive Cd accumulation features in the root-associated microbiome of two rice cultivars

Abstract

Developing low-cadmium (Cd) rice cultivars has emerged as a promising avenue for food safety in Cd-contaminated farmlands. The root-associated microbiomes of rice have been shown to enhance rice growth and alleviate Cd stress. However, the microbial taxon-specific Cd resistance mechanisms underlying different Cd accumulation characteristics between different rice cultivars remain largely unknown. This study compared low-Cd cultivar XS14 and hybrid rice cultivar YY17 for Cd accumulation with five soil amendments. The results showed that XS14 was characterized by more variable community structures and stable co-occurrence networks in the soil-root continuum compared to YY17. The stronger stochastic processes in assembly of the XS14 (~25%) rhizosphere community than that of YY17 (~12%) suggested XS14 may have higher resistance to changes in soil properties. Microbial co-occurrence networks and machine learning models jointly identified keystone indicator microbiota, such as Desulfobacteria in XS14 and Nitrospiraceae in YY17. Meanwhile, genes involved in sulfur cycling and nitrogen cycling were observed among the root-associated microbiome of these two cultivars, respectively. Microbiomes in the rhizosphere and root of XS14 showed a higher diversity in functioning, with the significant enrichment of functional genes related to amino acid and carbohydrate transport and metabolism, and sulfur cycling. Our findings revealed differences and similarities in the microbial communities associated with two rice cultivars, as well as bacterial biomarkers predictive of Cd-accumulation capacity. Thus, we provide new insights into taxon-specific recruitment strategies of two rice cultivars under Cd stress and highlight the utility of biomarkers in offering clues for enhancing crop resilience to Cd stresses in the future.

Cultivar-specific wheat-associated microbiomes and metabolites in response to nitrogen deficiency

“…2a). This is in line with a recent study that reported the variation of the relative abundance of the rhizosphere bacterial functional genes involved in multiple nutrient cycles between rice cultivars with different plant cadmium accumulation (Cheng et al 2023), supporting that crop cultivars have a predominant effect on the rhizobacteria functions. Further comparison of functional categories revealed that Mace has signi cantly enhanced rhizobacterial growth and motility under N de ciency, a phenomenon not observed in Gladius (Fig.…”

Endophytic bacterial communities of alpine Rosaceae plants are affected by the plant tissue, collection site and host plant and culturable psychrotolerant isolates contribute to plant freezing stress tolerance

“…Elymus nutans , Festuca sinensis , Kobresia pygmaea and Kobresia humilis ) (Liu et al ., 2021; Wei et al ., 2022) and it is possibly associated with competitive exclusion, historical contingency (i.e. result of a disturbance effect, such as recurrent frosts) and adaptability of bacterial endophytes to variation in environmental conditions, as suggested for other plant hosts (Cheng et al ., 2023; Cregger et al ., 2018; Hough et al ., 2020; Xie et al ., 2021; Zhu et al ., 2021; Bell et al ., 2022; Taniguchi et al ., 2023). However, the assembly of plant-associated bacterial communities can shift between stochastic and deterministic processes depending on plant genotype, age and growth stage (Dove et al ., 2021; Bell et al ., 2022; Wang et al ., 2023), indicating the possible contribution of both processes.…”

Evolutionary prediction for new echolocators

“…The use of machine learning methods to construct predictive models of biological traits based on molecular characteristics has been demonstrated to be effective, resulting in increased throughputs and reduced costs for subsequent research ( 30, 31 ). Our machine learning model allows us to identify new echolocating mammals on a large scale with only a limited number of convergent amino acids among known echolocating mammals.…”