This study revealed the efficient nutrient cycling mechanism of mangroves. Positive coupling effects were observed in sediment quality, NF and PS processes, and NFOPSMs with the invasion of S. alterniflora .

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Sulfur, organosulfur compounds, and sulfides are essential parts of life. Microbial sulfate assimilation is among the most active and ancient metabolic activities in the sulfur cycle that operates in various ecosystems. We analyzed the molecular basis of bacterial characterization. NR1 was isolated and purified from mangrove sediments. Whole-genome sequencing indicated that the NR1 isolate was closely related to Bacillus cereus. The genome contained 5,305 functional genes with a total length of 5,420,664 bp, a GC content of 35.62%, 42 rRNA, and 107 tRNA. DBT-grown cultures exhibited DBT utilization, fleeting emergence of DBT sulfone (DBTO2), and formation of 2-hydroxybiphenyl (2-HBP). Molecular analysis of the PCR products’ dsz operon revealed the presence of dszA, dszB, and dszC genes, which encoded for NR1’s 90% DBT desulfurization activity. Furthermore, 17 sulfur metabolism-related genes, including genes involved in assimilation sulfate reduction, APS and PAPS, and the cys, ssu, and TST gene families, were identified. In sulfate media, alkenesulfonate was converted to sulfite and inhibited ssu enzymes. Downregulated cysK variants were associated with nrnA expression and the regulation of L-cysteine synthesis. These findings established a scientific foundation for further research and application of bacteria to mangrove rehabilitation and ecological treatment by evaluating the bacterial characterization and sulfur degradation metabolic pathway. We used whole-genome and transcriptome sequencing to examine their genetic characteristics.

With the upgrade and development of the high-throughput sequencing technology, multi-omics data can be obtained at a low cost. However, mapping tools that existed for microbial multi-omics data analysis cannot satisfy the needs of data description and result in high learning costs, complex dependencies, and high fees for researchers in experimental biology fields. Therefore, developing a toolkit for multi-omics data is essential for microbiologists to save effort. In this work, we developed MicrobioSee, a real-time interactive visualization tool based on web technologies, which could visualize microbial multi-omics data. It includes 17 modules surrounding the major omics data of microorganisms such as the transcriptome, metagenome, and proteome. With MicrobioSee, methods for plotting are simplified in multi-omics studies, such as visualization of diversity, ROC, and enrichment pathways for DEGs. Subsequently, three case studies were chosen to represent the functional application of MicrobioSee. Overall, we provided a concise toolkit along with user-friendly, time-saving, cross-platform, and source-opening for researchers, especially microbiologists without coding experience. MicrobioSee is freely available at https://microbiosee.gxu.edu.cn.