Soil fungi play a critical role in plant performance and soil nutrient cycling. However, the understanding of soil fungal community composition and functions in response to different nutrients management practices in red soils remains largely unknown. Here, we investigated the responses of soil fungal communities and functions under conventional farmer fertilization practice (FFP) and different nutrient management practices, i.e., optimization of NPK fertilizer (O) with soil conditioner (O + C), with lime and mushroom residue (O + L + M), and with lime and magnesium fertilizer (O + L + Mg). Illumina high-throughput sequencing was used for fungal identification, while the functional groups were inferred with FUNGuild. Nutrient management practices significantly raised the soil pH to 4.79–5.31 compared with FFP (3.69), and soil pH had the most significant effect (0.989 ***) on fungal communities. Predominant phyla, including Ascomycota, Basidiomycota, and Mortierellomycota were identified in all treatments and accounted for 94% of all fungal communities. The alpha diversity indices significantly increased under nutrients management practices compared with FFP. Co-occurrence network analysis revealed the keystone fungal species in the red soil, i.e., Ascomycota (54.04%), Basidiomycota (7.58%), Rozellomycota (4.55%), and Chytridiomycota (4.04%). FUNGuild showed that the relative abundance of arbuscular mycorrhizal fungi and ectomycorrhizal fungi was higher, while pathogenic fungi were lower under nutrient management practices compared with FFP. Our findings have important implications for the understanding of improvement of acidic soils that could significantly improve the soil fungal diversity and functioning in acidic soils.

Common mycorrhizal networks (CMNs) allow the transfer of nutrients between plants, influencing the growth of the neighboring plants and soil properties. Cleistogene squarrosa (C. squarrosa) is one of the most common grass species in the steppe ecosystem of Inner Mongolia, where nitrogen (N) is often a key limiting nutrient for plant growth, but little is known about whether CMNs exist between neighboring individuals of C. squarrosa or play any roles in the N acquisition of the C. squarrosa population. In this study, two C. squarrosa individuals, one as a donor plant and the other as a recipient plant, were planted in separate compartments in a partitioned root-box. Adjacent compartments were separated by 37 µm nylon mesh, in which mycorrhizal hyphae can go through but not roots. The donor plant was inoculated with arbuscular mycorrhizal (AM) fungi, and their hyphae potentially passed through nylon mesh to colonize the roots of the recipient plant, resulting in the establishment of CMNs. The formation of CMNs was verified by microscopic examination and ¹⁵N tracer techniques. Moreover, different levels of N fertilization (N0 = 0, N1 = 7.06, N2 = 14.15, N3 = 21.19 mg/kg) were applied to evaluate the CMNs’ functioning under different soil nutrient conditions. Our results showed that when C. squarrosa–C. squarrosa was the association, the extraradical mycelium transferred the ¹⁵N in the range of 45–55% at different N levels. Moreover, AM fungal colonization of the recipient plant by the extraradical hyphae from the donor plant significantly increased the plant biomass and the chlorophyll content in the recipient plant. The extraradical hyphae released the highest content of glomalin-related soil protein into the rhizosphere upon N2 treatment, and a significant positive correlation was found between hyphal length and glomalin-related soil proteins (GRSPs). GRSPs and soil organic carbon (SOC) were significantly correlated with mean weight diameter (MWD) and helped in the aggregation of soil particles, resulting in improved soil structure. In short, the formation of CMNs in this root-box experiment supposes the existence of CMNs in the typical steppe plants, and CMNs-mediated N transfer and root colonization increased the plant growth and soil properties of the recipient plant.

Histone deacetylases (HDACs) play a significant role in a plant’s development and response to various environmental stimuli by regulating the gene transcription. However, HDACs remain unidentified in cotton. In this study, a total of 29 HDACs were identified in allotetraploid Gossypium hirsutum, while 15 and 13 HDACs were identified in Gossypium arboretum and Gossypium raimondii, respectively. Gossypium HDACs were classified into three groups (reduced potassium dependency 3 (RPD3)/HDA1, HD2-like, and Sir2-like (SRT) based on their sequences, and Gossypium HDACs within each subgroup shared a similar gene structure, conserved catalytic domains and motifs. Further analysis revealed that Gossypium HDACs were under a strong purifying selection and were unevenly distributed on their chromosomes. Gene expression data revealed that G. hirsutum HDACs were differentially expressed in various vegetative and reproductive tissues, as well as at different developmental stages of cotton fiber. Furthermore, some G. hirsutum HDACs were co-localized with quantitative trait loci (QTLs) and single-nucleotide polymorphism (SNPs) of fiber-related traits, indicating their function in fiber-related traits. We also showed that G. hirsutum HDACs were differentially regulated in response to plant hormones (abscisic acid (ABA) and auxin), DNA damage agent (methyl methanesulfonate (MMS)), and abiotic stresses (cold, salt, heavy metals and drought), indicating the functional diversity and specification of HDACs in response to developmental and environmental cues. In brief, our results provide fundamental information regarding G. hirsutum HDACs and highlight their potential functions in cotton growth, fiber development and stress adaptations, which will be helpful for devising innovative strategies for the improvement of cotton fiber and stress tolerance.

Malate dehydrogenase, which facilitates the reversible conversion of malate to oxaloacetate, is essential for energy balance, plant growth, and cold and salt tolerance. However, the genome-wide study of the MDH family has not yet been carried out in tomato (Solanum lycopersicum L.). In this study, 12 MDH genes were identified from the S. lycopersicum genome and renamed according to their chromosomal location. The tomato MDH genes were split into five groups based on phylogenetic analysis and the genes that clustered together showed similar lengths, and structures, and conserved motifs in the encoded proteins. From the 12 tomato MDH genes on the chromosomes, three pairs of segmental duplication events involving four genes were found. Each pair of genes had a Ka/Ks ratio < 1, indicating that the MDH gene family of tomato was purified during evolution. Gene expression analysis exhibited that tomato MDHs were differentially expressed in different tissues, at various stages of fruit development, and differentially regulated in response to abiotic stresses. Molecular docking of four highly expressed MDHs revealed their substrate and co-factor specificity in the reversible conversion process of malate to oxaloacetate. Further, co-localization of tomato MDH genes with quantitative trait loci (QTL) of salt stress-related phenotypes revealed their broader functions in salt stress tolerance. This study lays the foundation for functional analysis of MDH genes and genetic improvement in tomato.

The process of etiolation contributes significantly to vegetative propagation and root formation of woody plants. However, the molecular interaction pattern of different factors for etiolated adventitious root development in woody plants remains unclear. In the present study, we explored the changes at different etiolation stages of adventitious root formation in Robinia pseudoacacia. Histological and transcriptomic analyses were performed for the etiolated lower portion of hypocotyls to ascertain the adventitious root responses. We found that the dark-treated hypocotyls formed roots earlier than the control. Exogenous application of NAA (0.3 mg/L) stimulated the expressions of about 310 genes. Among these, 155 were upregulated and 155 were downregulated. Moreover, differentially expressed genes (DEGs) were significantly enriched in multiple pathways, including the biosynthesis of secondary metabolites, metabolic pathway, plant hormone signal transduction, starch and sucrose metabolism, phenylpropanoid biosynthesis, and carbon metabolism. These pathways could play a significant role during adventitious root formation in etiolated hypocotyls. The findings of this study can provide novel insights and a foundation for further studies to elucidate the connection between etiolation and adventitious root formation in woody plants.