Comparative Genomics of Lotus japonicus Reveals Insights into Proanthocyanidin Accumulation and Abiotic Stress Response.

Lotus japonicus, is an important perennial model legume, has been widely used for studying biological processes such as symbiotic nitrogen fixation, proanthocyanidin (PA) biosynthesis, and abiotic stress response. High-quality L. japonicus genomes have been reported recently; however, the genetic basis of genes associated with specific characters including proanthocyanidin distribution in most tissues and tolerance to stress has not been systematically explored yet. Here, based on our previous high-quality L. japonicus genome assembly and annotation, we compared the L. japonicus MG-20 genome with those of other legume species. We revealed the expansive and specific gene families enriched in secondary metabolite biosynthesis and the detection of external stimuli. We suggested that increased copy numbers and transcription of PA-related genes contribute to PA accumulation in the stem, petiole, flower, pod, and seed coat of L. japonicus. Meanwhile, According to shared and unique transcription factors responding to five abiotic stresses, we revealed that MYB and AP2/ERF play more crucial roles in abiotic stresses. Our study provides new insights into the key agricultural traits of L. japonicus including PA biosynthesis and response to abiotic stress. This may provide valuable gene resources for legume forage abiotic stress resistance and nutrient improvement.

Effect of Biogas Slurry on the Soil Properties and Microbial Composition in an Annual Ryegrass-Silage Maize Rotation System over a Five-Year Period.

Soil health is seriously threatened by the overuse of chemical fertilizers in agricultural management. Biogas slurry is often seen as an organic fertilizer resource that is rich in nutrients, and its use has the goal of lowering the amount of chemical fertilizers used while preserving crop yields and soil health. However, the application of continuous biogas slurry has not yet been studied for its long-term impact on soil nutrients and microbial communities in a rotation system of annual ryegrass-silage maize (Zea mays). This study aimed to investigate the impacts on the chemical properties and microbial community of farmland soils to which chemical fertilizer (NPK) (225 kg ha-1), biogas slurry (150 t ha-1), and a combination (49.5 t ha-1 biogas slurry + 150 kg ha-1 chemical fertilizer) were applied for five years. The results indicated that compared to the control group, the long-term application of biogas slurry significantly increased the SOC, TN, AP, and AK values by 45.93%, 39.52%, 174.73%, and 161.54%, respectively; it neutralized acidic soil and increased the soil pH. TN, SOC, pH, and AP are all important environmental factors that influence the structural composition of the soil's bacterial and fungal communities. Chemical fertilizer application significantly increased the diversity of the bacterial community. Variation was observed in the composition of soil bacterial and fungal communities among the different treatments. The structure and diversity of soil microbes are affected by different methods of fertilization; the application of biogas slurry not only increases the contents of soil nutrients but also regulates the soil's bacterial and fungal community structures. Therefore, biogas slurry can serve as a sustainable management measure and offers an alternative to the application of chemical fertilizers for sustainable intensification.

The first two whole mitochondrial genomes for the genus Dactylis species: assembly and comparative genomics analysis.

BACKGROUND: Orchardgrass (Dactylis glomerata L.), a perennial forage, has the advantages of rich leaves, high yield, and good quality and is one of the most significant forage for grassland animal husbandry and ecological management in southwest China. Mitochondrial (mt) genome is one of the major genetic systems in plants. Studying the mt genome of the genus Dactylis could provide more genetic information in addition to the nuclear genome project of the genus. RESULTS: In this study, we sequenced and assembled two mitochondrial genomes of Dactylis species of D. glomerata (597, 281 bp) and D. aschersoniana (613, 769 bp), based on a combination of PacBio and Illumina. The gene content in the mitochondrial genome of D. aschersoniana is almost identical to the mitochondrial genome of D. glomerata, which contains 22-23 protein-coding genes (PCGs), 8 ribosomal RNAs (rRNAs) and 30 transfer RNAs (tRNAs), while D. glomerata lacks the gene encoding the Ribosomal protein (rps1) and D. aschersoniana contains one pseudo gene (atp8). Twenty-three introns were found among eight of the 30 protein-coding genes, and introns of three genes (nad 1, nad2, and nad5) were trans-spliced in Dactylis aschersoniana. Further, our mitochondrial genome characteristics investigation of the genus Dactylis included codon usage, sequences repeats, RNA editing and selective pressure. The results showed that a large number of short repetitive sequences existed in the mitochondrial genome of D. aschersoniana, the size variation of two mitochondrial genomes is due largely to the presence of a large number of short repetitive sequences. We also identified 52-53 large fragments that were transferred from the chloroplast genome to the mitochondrial genome, and found that the similarity was more than 70%. ML and BI methods used in phylogenetic analysis revealed that the evolutionary status of the genus Dactylis. CONCLUSIONS: Thus, this study reveals the significant rearrangements in the mt genomes of Pooideae species. The sequenced Dactylis mt genome can provide more genetic information and improve our evolutionary understanding of the mt genomes of gramineous plants.

Inoculation of Newborn Lambs with Ruminal Solids Derived from Adult Goats Reprograms the Development of Gut Microbiota and Serum Metabolome and Favors Growth Performance.

Microbial transplantation in early life was a strategy to optimize the health and performance of livestock animals. This study aimed to investigate the effect of active ruminal solids microorganism supplementation on newborn lamb gut microbiota and serum metabolism. Twenty-four Youzhou dark newborn lambs were randomly divided into three groups: (1) newborn lambs fed with sterilized goat milk inoculated with sterilized normal saline (CON), supernatant from ruminal solids (SRS), or autoclaved supernatant from ruminal solids (ASRS). Results showed that SRS increased gut bacterial richness and community, downregulating the Firmicutes/Bacteroidetes ratio, and increased the abundance of some probiotics (Bacteroidetes, Spirochaetota, and Fibrobacterota), while reducing the abundance of Fusobacteriota, compared to the CON group. SRS also improved the plasma metabolic function, such as arachidonic acid metabolism, primary bile acid biosynthesis, and tryptophan metabolism and then actively promoted the levels of ALP and HLD. Our study indicated that inoculation with active ruminal solids significantly affected the intestinal microbial communities and metabolic characteristics, and these changes can improve the growing health of the newborn lamb. These findings provided an experimental and theoretical basis for the application of ruminal solid-attached microorganisms in the nutritional management of lambs reared for human consumption.

Effect of different dry matter content on fermentation characteristics and nutritional quality of Napier grass silage with novel lactic acid bacteria strains.

To investigate the characteristics of different LAB strains isolated from subtropics and their effects on Napier grass (Pennisetum purpureum Schum.) silage with two dry matter (DM) levels, sugar fermentation pattern, and growth profiles of three screened lactic acid bacteria (LAB) strains [Pediococcus pentosaceus (PP04), Weissella cibaria (WC10), and Lactobacillus plantarum (LP694)] were characterized, and then used either individually or in combination at 1.0 × 106 cfu g-1 fresh weight to inoculate grass having 15% or 25% DM. Treatments were applied: (1) no inoculant (control); (2) PP04; (3) WC10; (4) LP694; (5) M-1 (PP04: WC10 = 2:1); (6) M-2 (PP04: LP694 = 1:2); (7) M-3 (WC10: LP694 = 2:1); (8) M-4 (PP04: WC10: LP694 = 2:1:1). The results showed that all inoculations increased LAB, DM recovery, and lactic acid (LA) concentration, while decreasing pH, the ammonia nitrogen/total nitrogen (NH3-N/TN), and butyric acid (BA) concentration compared to control group in both DM. However, the effect of inoculations was very limited at 15% DM. Silages with inoculants achieved higher silage quality at 25% DM than 15% DM. The different LAB inoculants result in significant differences in silage quality, while W. cibaria decreased the pH and inhibited the growth of undesirable bacteria and those characteristics were not affected by the DM content.

Single-cell RNA-seq of Lotus japonicus provide insights into identification and function of root cell types of legume.

The roots of legume plant play a crucial role in nitrogen fixation. However, the transcriptomes of different cell types of legume root and their functions remain largely unknown. Here, we performed single-cell RNA sequencing and profiled more than 22,000 single cells from root tips of Lotus japonicus, a model species of legume. We identified seven clusters corresponding to seven major cell types, which were validated by in situ hybridization. Further analysis revealed regulatory programs including phytohormone and nodulation associated with specific cell types, and revealed conserved and diverged features for the cell types. Our results represent the first single-cell resolution transcriptome for legume root tips and a valuable resource for studying the developmental and physiological functions of various cell types in legumes.

Genome-Wide Identification and Expression Profile of the HD-Zip Transcription Factor Family Associated with Seed Germination and Abiotic Stress Response in Miscanthus sinensis.

Miscanthus sinensis is an ornamental grass, non-food bioenergy crop, and forage with high feeding value. It can adapt to many kinds of soil conditions due to its high level of resistance to various abiotic stresses. However, a low level of seed germination restricts the utilization and application of M. sinensis. It is reported that the Homeodomain-leucine zipper (HD-Zip) gene family participates in plant growth and development and ability to cope with outside environment stresses, which may potentially regulate seed germination and stress resistance in M. sinensis. In this study, a complete overview of M. sinensis HD-Zip genes was conducted, including gene structure, conserved motifs, chromosomal distribution, and gene duplication patterns. A total of 169 members were identified, and the HD-Zip proteins were divided into four subgroups. Inter-chromosomal evolutionary analysis revealed that four pairs of tandem duplicate genes and 72 segmental duplications were detected, suggesting the possible role of gene replication events in the amplification of the M. sinensis HD-Zip gene family. There was an uneven distribution of HD-Zip genes on 19 chromosomes of M. sinensis. Also, evolutionary analysis showed that M. sinensis HD-Zip gene family members had more collinearity with monocotyledons and less with dicotyledons. The gene structure analysis showed that there were 93.5% of proteins with motif 1 and motif 4, while motif 10 was only found in group IV. Based on the cis-elements analysis, it appeared that most of the genes were related to plant growth and development, various hormones, and abiotic stress. Furthermore, qRT-PCR analysis showed that Misin06G303300.1 was significantly expressed in seed germination and Misin05G030000.1 and Misin06G303300.1 were highly expressed under chromium, salt, and drought stress. Results in this study will provide a basis for further exploring the potential role of HD-Zip genes in stress responses and genetic improvement of M. sinensis seed germination.

Microbial Community and FermentationDynamics of Corn Silage Prepared withHeat-Resistant Lactic Acid Bacteria in a HotEnvironment.

To develop a silage fermentation technique to adapt to global climate changes, the microbiome and fermentation dynamics of corn silage inoculated with heat-resistant lactic acid bacteria (LAB) under high-temperature conditions were studied. Corn was ensiled in laboratory silo, with and without two selected strains, Lactobacillus salivarius LS358 and L. rhamnosus LR753, two type strains L. salivarius ATCC 11741Tand L. rhamnosus ATCC 7469T. The ensiling temperatures were designed at 30 °C and 45 °C, and the sampling took place after 0, 3, 7, 14, and 60 days of fermentation. The higher pH and dry matter losses were observed in the silages stored at 45 °C compared to those stored at 30 °C. Silages inoculated with strains LS358 and LR753 at 30 °C had a lower ratio of lactic acid/acetic acid. The dominant bacterial genera gradually changed from Pediococcus and Lactobacillus to Lactobacillus in silages during ensiling at 30 °C, while the bacterial community became more complex and fragmented after 7 d of ensiling at 45 °C. The high temperatures significantly led to a transformation of the LAB population from homo-fermentation to hetero-fermentation. This study is the first to describe microbial population dynamics response to high temperature during corn ensiling, and the results indicate that L. rhamnosus 753 shows potential ability to improve silage fermentation in tropics and subtropics. bacteria community; fermentation dynamics; high temperature; lactic acidbacteria; corn silage.

Microbial communities and natural fermentation of corn silages prepared with farm bunker-silo in Southwest China.

This study analyzed the variation of microbial communities, their achieved fermentation quality, and the association between microbial diversity and environmental factors after ensiling of 96 samples prepared with bunker-silo in Southwest China. Most of natural corn silages achieved good fermentation, e.g., low pH value (<4.2) and high levels of lactic acid (36.26-79.83 mg/g DM). Weissella species were the dominant epiphytic bacteria in raw material, while Lactobacillus and Acetobacter species were prevalent in silages. Natural Lactobacillus and Pediococcus species produced more lactic acid during ensiling, while the production of acetic acid was highly positively correlated with both Acetobacter and Bradyrhizobium species. Rainfall and humidity affected community of epiphytic bacteria on the corn material, and the temperature affected richness of bacterial species during ensiling. The results confirmed that microbial community of silages in hot and humid area is unique and climatic factors ultimately affect the fermentation quality through influencing microbial community.