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PubMed2024

Comparative genomic analysis and functional investigations for MCs catabolism mechanisms and evolutionary dynamics of MCs-degrading bacteria in ecology.

Microcystins (MCs) significantly threaten the ecosystem and public health. Biodegradation has emerged as a promising technology for removing MCs. Many MCs-degrading bacteria have been identified, including an indigenous bacterium Sphingopyxis sp. YF1 that could degrade MC-LR and Adda completely. Herein, we gained insight into the MCs biodegradation mechanisms and evolutionary dynamics of MCs-degrading bacteria, and revealed the toxic risks of the MCs degradation products. The biochemical characteristics and genetic repertoires of strain YF1 were explored. A comparative genomic analysis was performed on strain YF1 and six other MCs-degrading bacteria to investigate their functions. The degradation products were investigated, and the toxicity of the intermediates was analyzed through rigorous theoretical calculation. Strain YF1 might be a novel species that exhibited versatile substrate utilization capabilities. Many common genes and metabolic pathways were identified, shedding light on shared functions and catabolism in the MCs-degrading bacteria. The crucial genes involved in MCs catabolism mechanisms, including mlr and paa gene clusters, were identified successfully. These functional genes might experience horizontal gene transfer events, suggesting the evolutionary dynamics of these MCs-degrading bacteria in ecology. Moreover, the degradation products for MCs and Adda were summarized, and we found most of the intermediates exhibited lower toxicity to different organisms than the parent compound. These findings systematically revealed the MCs catabolism mechanisms and evolutionary dynamics of MCs-degrading bacteria. Consequently, this research contributed to the advancement of green biodegradation technology in aquatic ecology, which might protect human health from MCs.

Humans↗

PubMed2026

Microbial aerobic degradation of 4-isopropylnitrobenzene by Sphingobium yanoikuyae strain SG1.

4-Isopropylnitrobenzene (4-IPNB) is a nitroaromatic compound commonly employed as an intermediate in pesticide synthesis and chemical manufacturing. Despite its potential environmental persistence and ecological risks, the microbial degradation pathway of 4-IPNB remains largely unknown. In this study, a Gram-negative bacterium, designated Sphingobium yanoikuyae strain SG1, was isolated from a pesticide manufacturing site in Brazil for its ability to utilize 4-IPNB as the sole added source of carbon, nitrogen, and energy. Aerobic degradation of 4-IPNB by strain SG1 was accompanied by nitrite release, and intermediate-trapping experiments revealed the transient accumulation of 4-isopropylcatechol (4-IPC). Together, these findings support the initial conversion of 4-IPNB to 4-IPC through oxidative denitration and dihydroxylation. Genomic and transcriptomic analyses further inferred several candidate nitroarene dioxygenases that may catalyze this initial reaction. Furthermore, the downstream metabolism of 4-IPC proceeded via both meta- and ortho-cleavage pathways, with cell-extract enzyme assays demonstrating predominant meta-cleavage activity under the tested conditions. Strain SG1 also degraded 4-IPNB in nonsterile soil slurry microcosms, extending its degradation capability beyond defined liquid culture. This study provides the first comprehensive insight into the microbial aerobic degradation of 4-IPNB, advances our understanding of the environmental fate of emerging nitroaromatic contaminants, and supports the potential of strain SG1 in 4-IPNB biodegradation and removal.

Sphingomonadaceae↗

PubMed2025

Sphingobium yanoikuyae 41R9 Enhances Nitrogen Uptake by Modulating Transporter Genes and Root Development in Rapeseed.

Plant growth-promoting rhizobacteria (PGPR) are widely recognized for enhancing the absorption of mineral nutrients by crops. While Sphingobium species have been reported as PGPRs, their capacity to improve nitrogen use efficiency (NUE) and the underlying regulatory mechanisms are not yet fully understood. Here, a strain 41R9, isolated from the rhizosphere of N-deficient rapeseed, was found to significantly enhance the growth performance of rapeseed under both low and normal N conditions. Genomic analysis revealed that strain 41R9 was closely related to Sphingobium yanoikuyae. 15N isotope tracer experiments confirmed that inoculation with strain 41R9 significantly boosted N uptake and translocation in rapeseed roots. Transcriptome profiling demonstrated that strain 41R9 directly upregulated N transporter genes (NRT2.5 and SLAH1/3), facilitating efficient N acquisition. Furthermore, strain 41R9 maintained jasmonic acid (JA) homoeostasis via JAZ-mediated negative feedback, balancing defense responses and root development, thereby improving the plant's N acquisition capacity in the roots. Metabolomic and in vitro assays further demonstrated that strain 41R9 displayed strong chemotaxis towards kaempferol, a N-deficiency-induced root exudate, suggesting kaempferol might as a chemical effector for S. yanoikuyae recruitment. These findings advance our understanding of PGPR-driven mechanisms in enhancing crop NUE and highlight the potential of harnessing PGPRs for sustainable agriculture.

Plant Roots↗