Class III peroxidases (PODs), commonly known as secretable class III plant peroxidases, are plant-specific enzymes that play critical roles in not only plant growth and development but also the responses to biotic and abiotic stress. In this study, we identified 198 nonredundant POD genes, designated GhPODs, with 180 PODs being predicted to secrete into apoplast. These POD genes were divided into 10 sub-groups based on their phylogenetic relationships. We performed systematic bioinformatic analysis of the POD genes, including analysis of gene structures, phylogenetic relationships, and gene expression profiles. The GhPODs are unevenly distributed on both upland cotton sub-genome A and D chromosomes. Additionally, these genes have undergone 15 segmental and 12 tandem duplication events, indicating that both segmental and tandem duplication contributed to the expansion of the POD gene family in upland cotton. Ka/Ks analysis suggested that most duplicated GhPODs experienced negative selection, with limited functional divergence during the duplication events. High-throughput RNA-seq data indicated that most highly expressed genes might play significant roles in root, stem, leaf, and fiber development. Under K or P deficiency conditions, PODs showed different expression patterns in cotton root and leaf. This study provides useful information for further functional analysis of the POD gene family in upland cotton.

The simultaneous presence of microplastics (MPs) and heavy metals in soil may result in heightened toxicity, causing more significant adverse effects on plant growth. Plant growth-promoting rhizobacteria (PGPR) have demonstrated significant capacities in alleviating the toxic stress caused by the combined pollution of heavy metals and other contaminants. However, research on the impacts and processes of PGPR in alleviating stress induced by the combined pollution from MPs and heavy metals is still insufficient. This study involved a pot experiment to evaluate the ability of PGPR to mitigate stress induced by the combined pollution from polypropylene microplastic (PP MPs) particles of different sizes (6.5 μm and 830 μm) and the heavy metal cadmium (Cd) in the bioenergy plant hybrid Pennisetum. Moreover, metagenomic analysis was used to examine the effects of PGPR on the rhizospheric microbial community and function. The cocontamination of PP and Cd affected the growth of the hybrid Pennisetum differently depending on the size of the MPs particles, with the aboveground and underground lengths of the 6.5 μm PP + Cd experimental group being smaller than those of the 830 μm PP + Cd group. The PGPRs (Bacillus sp. Y-35, Bacillus sp. Y-62, Bacillus sp. Y-S, and Enterobacter sp. Y-V) successfully alleviated the stress caused by the combined pollution of PP and Cd, resulting in increases of 8.24 and 42.21% in the plant height and dry weight, respectively. The metagenomic studies indicated that the cocontamination of PP and Cd, along with PGPR inoculation, altered the composition of the rhizospheric bacterial community, leading to changes in microbial diversity indices and the composition of dominant groups such as Pseudomonadota, Actinomycetota, and Acidobacteriota. The functional analysis revealed that the main functional groups involved glucose metabolism, energy metabolism, signal transduction, and nucleotide metabolism. The MPs particle size and different PGPR significantly affected functions such as the pentose phosphate pathway, benzoate degradation, and amide biosynthesis. This study provides essential data and scientific evidence on the ecotoxicological effects of simultaneous contamination by MPs and heavy metals, as well as insights into potential bioremediation methods.

Microplastics (MPs) and heavy metals are commonly present in soil at significant concentrations and can interact in complex ways that pose serious threats to environmental and ecological systems. The effects of combined contamination by different types of heavy metals and microplastics on plants, as well as on soil microbial communities and their functions, remain largely unexplored. In this study, a series of pot experiments was conducted to investigate the effects of composite contamination involving two heavy metals (Cd and Pb) and two types of microplastics polylactic acid (PLA) and polybutylene succinate (PBS) at varying concentrations (0.1% and 0.5%, w/w). The impacts on water spinach (Ipomoea aquatica) growth and heavy metal accumulation were evaluated, and the rhizosphere bacterial and fungal community structure and diversity were analyzed using high-throughput sequencing. The presence of Cd, Pb, and microplastics significantly inhibited the growth of water spinach, reducing both its length and biomass. Under combined microplastic–heavy metal contamination, phytotoxicity increased with rising concentrations of PLA and PBS. Microplastics were found to alter the mobility and availability of heavy metals, thereby reducing their accumulation in plant tissues and decreasing the levels of available potassium and phosphorus in the soil. Furthermore, microplastic–heavy metal interactions significantly influenced the composition and diversity of soil microbial communities, leading to an increased abundance of heavy-metal-tolerant and potential plastic-degrading microorganisms. A strong correlation was observed between microbial community structure (both bacterial and fungal), soil physicochemical properties, and plant growth. Functional predictions using PICRUSt2 suggested that the type and concentration of microplastics significantly affected rhizosphere microorganisms’ metabolic functions. In conclusion, the present study demonstrates that combined microplastic and heavy metal contamination exerts a detrimental effect on soil nutrient availability, resulting in alterations to soil microbial community composition and function. Furthermore, this study shows that these contaminants can inhibit plant growth and heavy metal uptake. The findings provide a valuable contribution to the existing body of knowledge on the ecotoxicological impacts of microplastic–heavy metal composite pollution in terrestrial ecosystems.

Drought is a major abiotic stress in restricting the growth, development, and yield of maize. As a significant epigenetic regulator, small RNA also functions in connecting the transcriptional and post-transcriptional regulatory network. Further to help comprehending the molecular mechanisms underlying drought adaptability and tolerance of maize, an integrated multi-omics analysis of transcriptome, sRNAome, and degradome was performed on the seedling roots of an elite hybrid Zhengdan958 under drought stress. In this study, 2,911 genes, 32 conserved miRNAs, and 12 novel miRNAs showed a significantly differential expression under drought stress. Moreover, 6,340 target genes of 445 miRNAs were validated using degradome sequencing, forming 281 miRNA–mRNA pairs in control (CK) and drought-stressed (DS) library. These target genes were mainly involved in the plant hormone signal transduction and phenylpropanoid biosynthesis pathways. The integrated multi-omics analysis revealed that five DEmiRNA–mRNA pairs displayed negatively correlated expression patterns, which were also verified by qRT-PCR. Tissue-specific expression profile and regulatory network analysis revealed that miR528a/b- Zm00001d021850 , miR408a/b- Zm00001d020794 , and miR164e- Zm00001d003414 might be essential in root-specific drought stress response of maize Zhengdan958 seedlings. These worthwhile will promote the functional characterization of miRNA–mRNA modules response to drought stress, and potentially contribute to drought-resistance breeding of maize.

Residue incorporation is a universally accepted agronomic practice around the world. However, the relationship between C and N turnover in soil is still not fully understood. We performed a soil microcosm incubation experiment to study the effects of residue incorporation with different C-to-N ratios (C/N) (low, 31.8; high, 84.5) on the SOC distribution, diazotrophic bacterial composition, and N accumulation in different particle size fractions (PSFs) of three types of soil parent material with different native C/N ratios. Our results demonstrate that SOC is 1.34 to 2.50 times more easily retained and accumulated in clay compared to baseline levels at the early stage of soil development. The native C/N ratio markedly affects the microbial metabolic characteristics and the SOC accumulation processes. Specifically, low C/N residue enhanced SOC accumulation in high-native-C/N soil, while the high-C/N residue maximized SOC in low-native-C/N soil. These shifts regulated the composition of the diazotrophic bacterial community, increasing the nitrogenase coding gene (nifH) abundance 5.57- and 8.1-fold in low-C/N residue treatments and 6.6-fold in the high-C/N residue treatment, thereby promoting soil N accumulation. Moreover, we highlight the potential role of Bradyrhizobiaceae, Rhodospirillaceae, Micrococcaceae, Rhizobiaceae, Comamonadaceae, Nitrospiraceae, and Burkholderiaceae in biological N fixation during pedogenesis. This study explored the coupling relationship between soil native and residue C/N and soil biological N fixation at the soil particle level, and the results suggest that residue incorporation to improve soil fertility needs to be further explored according to soil native C/N.

Studies have shown that abundant and various flavonoids accumulate in chili pepper (Capsicum), but there are few reports on the genes that govern chili pepper flavonoid biosynthesis. Here, we report the comprehensive identification of genes encoding type III polyketide synthase (PKS), an important enzyme catalyzing the generation of flavonoid backbones. In total, 13, 14 and 13 type III PKS genes were identified in each genome of C. annuum, C. chinense and C. baccatum, respectively. The phylogeny topology of Capsicum PKSs is similar to those in other plants, as it showed two classes of genes. Within each class, clades can be further identified. Class II genes likely encode chalcone synthase (CHS) as they are placed together with the Arabidopsis CHS gene, which experienced extensive expansions in the genomes of Capsicum. Interestingly, 8 of the 11 Class II genes form three clusters in the genome of C. annuum, which is likely the result of tandem duplication events. Four genes are not expressed in the tissues of C. annuum, three of which are located in the clusters, indicating that a portion of genes was pseudogenized after tandem duplications. Expression of two Class I genes was complementary to each other, and all the genes in Class II were not expressed in roots of C. annuum. Two Class II genes (CA00g90790 and CA05g17060) showed upregulated expression as the chili pepper leaves matured, and two Class II genes (CA05g17060 and CA12g20070) showed downregulated expression with the maturation of fruits, consistent with flavonoid accumulation trends in chili pepper as reported previously. The identified genes, sequences, phylogeny and expression information collected in this article lay the groundwork for future studies on the molecular mechanisms of chili pepper flavonoid metabolism.