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<jats:p>Anti-nutritional factors (ANFs) substances in plant products, such as indigestible non-starchy polysaccharides (α-galactooligosaccharides, α-GOS), phytate, tannins, and alkaloids can impede the absorption of many critical nutrients and cause major physiological disorders. To enhance silage quality and its tolerance threshold for humans as well as other animals, ANFs must be reduced. This study aims to identify and compare the bacterial species/strains that are potential use for industrial fermentation and ANFs reduction. A pan-genome study of 351 bacterial genomes was performed, and binary data was processed to quantify the number of genes involved in the removal of ANFs. Among four pan-genomes analysis, all 37 tested <jats:italic>Bacillus subtilis</jats:italic> genomes had one phytate degradation gene, while 91 out of 150 Enterobacteriacae genomes harbor at least one genes (maximum three). Although, no gene encoding phytase detected in genomes of <jats:italic>Lactobacillus</jats:italic> and <jats:italic>Pediococcus</jats:italic> species, they have genes involving indirectly in metabolism of phytate-derivatives to produce Myo-inositol, an important compound in animal cells physiology. In contrast, genes related to production of lectin, tannase and saponin degrading enzyme did not include in genomes of <jats:italic>B. subtilis</jats:italic> and <jats:italic>Pediococcus </jats:italic>species. Our findings suggest a combination of bacterial species and/or unique strains in fermentation, for examples, two Lactobacillus strains (DSM 21115 and ATCC 14869) with <jats:italic>B. subtilis</jats:italic> SRCM103689, would maximize the efficiency in reducing the ANFs concentration. In conclusion, this study provides insights into bacterial genomes analysis for maximizing nutritional value in plant-based food. Further investigations of gene numbers and repertories correlated to metabolism of different ANFs will help clarifying the efficiency of time consuming and food qualities.</jats:p>

<jats:sec><jats:title>Introduction</jats:title><jats:p>Symbiotic N fixation inhibition induced by N supply to legumes is potentially regulated by the relative N and P availability in soil. However, the specific responses of different legume species to changes in N:P availability remain unclear, and must be better understood to optimize symbiotic N fixation inputs under N enrichment. This study investigated mechanisms by which soil N and P supply influence the symbiotic N fixation of eight legume species, to quantify the inter-specific differences, and to demonstrate how these differences can be determined by the stoichiometric homeostasis in N:P ratios (H<jats:sub>N:P</jats:sub>).</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>Eight herbaceous legume species were grown separately in outdoor pots and treated with either no fertilizer (control), N fertilizer (14 g N m<jats:sup>-2</jats:sup>), P fertilizer (3.5 g P m<jats:sup>-2</jats:sup>) or both N and P fertilizer. Plant nutrients, stoichiometric characteristics, root biomass, non-structural carbohydrates (NSC), rhizosphere chemistry, P mobilization, root nodulation and symbiotic N fixation were measured.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>N addition enhanced rhizosphere P mobilization but drove a loss of root biomass and root NSC <jats:italic>via</jats:italic> exudation of P mobilization compound (organic acid), especially so in treatments without P addition. N addition also induced a 2-14% or 14-36% decline in symbiotic N fixation per plant biomass by legumes in treatments with or without P addition, as a result of decreasing root biomass and root NSC. The changes in symbiotic N fixation were positively correlated with stoichiometric homeostasis of N:P ratios in intact plants without root nodules, regardless of P additions.</jats:p></jats:sec><jats:sec><jats:title>Discussion</jats:title><jats:p>This study indicates that N addition can induce relative P limitations for growth, which can stimulate rhizosphere P mobilization at the expense of root biomass and carbohydrate concentrations, reducing symbiotic N fixation in legumes. Legume species that had less changes in plant N:P ratio, such as <jats:italic>Lespedeza daurica and Medicago varia</jats:italic> maintained symbiotic N fixation to a greater extent under N addition.</jats:p></jats:sec>

<jats:p>The highly diverse Colombian Central Collection (CCC) of cultivated potatoes is the most important source of genetic variation for breeding and the agricultural development of this staple crop in Colombia. Potato is the primary source of income for more than 100.000 farming families in Colombia. However, biotic and abiotic challenges limit crop production. Furthermore, climate change, food security, and malnutrition constraints call for adaptive crop development to be urgently addressed. The clonal CCC of potatoes contains 1,255 accessions ― an extensive collection size that limits its optimal assessment and use. Our study evaluated different collection sizes from the whole clonal collection to define the best core collection that captures the total genetic diversity of this unique collection, to support a characterization more cost-effectively. Initially, we genotyped 1,141 accessions from the clonal collection and 20 breeding lines using 3,586 genome-wide polymorphic markers to study CCC’s genetic diversity. The analysis of molecular variance confirmed the CCC’s diversity with a significant population structure (Phi=0.359; <jats:italic>p-value</jats:italic>=0.001). Three main genetic pools were identified within this collection (CCC_Group_A, CCC_Group_B1, and CCC_Group_B2), and the commercial varieties were located across the pools. The ploidy level was the main driver of pool identification, followed by a robust representation of accessions from Phureja and Andigenum cultivar groups based on former taxonomic classifications. We also found divergent heterozygosity values within genetic groups, with greater diversity in genetic groups with tetraploids (CCC_Group_B1: 0.37, and CCC_Group_B2: 0.53) than in diploid accessions (CCC_Group_A: 0.14). We subsequently generated one mini-core collection size of 3 percent (39 entries) and three further core collections sizes of 10, 15, and 20 percent (i.e., 129, 194, and 258 entries, respectively) from the total samples genotyped. As our results indicated that genetic diversity was similar across the sampled core collection sizes compared to the main collection, we selected the smallest core collection size of 10 percent. We expect this 10 percent core collection to be an optimal tool for discovering and evaluating functional diversity in the genebank to advance potato breeding and agricultural-related studies. This study also lays the foundations for continued CCC curation by evaluating duplicity and admixing between accessions, completing the digitalization of data, and ploidy determination using chloroplast count. </jats:p>

<jats:sec><jats:title>Introduction</jats:title><jats:p>Unfavorable coastal saline-alkali soil habitats degrade plant community diversity and reduce terrestrial ecological functions. Previous studies have been conducted on the mechanisms by which certain saline-alkali soil properties determine plant community diversity, however, how those properties synergistically affect plant community diversity remains unclear.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>Here, 36 plots of typical <jats:italic>Tamarix chinensis</jats:italic> communities were investigated for a range of parameters at three different distances (10, 20, and 40 km) from the coastline in the Yellow River Delta between 2020 and 2022, and corresponding soil samples were taken and analyzed.</jats:p></jats:sec><jats:sec><jats:title>Results and discussion</jats:title><jats:p>Our results suggest that although <jats:italic>T. chinensis</jats:italic> density, ground diameter, and canopy coverage significantly increased (<jats:italic>P</jats:italic>&amp;lt;0.05) with increasing distance from the coast, the communities with the most plant species were found at 10 to 20 km distance from the coastline, indicating the effects of soil habitat on <jats:italic>T. chinensis</jats:italic> community diversity. Simpson dominance (species dominance), Margalef (species richness), and Pielou indices (species evenness) differed significantly among the three distances (<jats:italic>P</jats:italic>&amp;lt;0.05) and were significantly correlated with soil sand content, mean soil moisture, and electrical conductivity (<jats:italic>P</jats:italic>&amp;lt;0.05), indicating that soil texture, water, and salinity were the main factors governing <jats:italic>T. chinensis</jats:italic> community diversity. Principal component analysis (PCA) was performed to construct an integrated soil habitat index (SHI) representing the synthesis of the soil texture-water-salinity condition. The estimated SHI quantified a 64.2% variation in the synthetic soil texture-water-salinity condition and was significantly higher at the 10 km distance than at the 40 and 20 km distances. The SHI linearly predicted <jats:italic>T. chinensis</jats:italic> community diversity (R<jats:sup>2</jats:sup> = 0.12–0.17, <jats:italic>P</jats:italic>&amp;lt;0.05), suggesting that greater SHI (coarser soil texture, wetter soil moisture regime, and higher soil salinity) was found closer to the coast and coincided with higher species dominance and evenness and lower species richness in the <jats:italic>T. chinensis</jats:italic> community. These findings on the relationship between <jats:italic>T. chinensis</jats:italic> communities and soil habitat conditions will be valuable in planning the restoration and protection of the ecological functions of <jats:italic>T. chinensis</jats:italic> shrubs in the Yellow River Delta.</jats:p></jats:sec>

<jats:p>Panicle development is crucial to increase the grain yield of rice (<jats:italic>Oryza sativa</jats:italic>). The molecular mechanisms of the control of panicle development in rice remain unclear. In this study, we identified a mutant with abnormal panicles, termed <jats:italic>branch one seed 1-1</jats:italic> (<jats:italic>bos1-1</jats:italic>). The <jats:italic>bos1-1</jats:italic> mutant showed pleiotropic defects in panicle development, such as the abortion of lateral spikelets and the decreased number of primary panicle branches and secondary panicle branches. A combined map-based cloning and MutMap approach was used to clone <jats:italic>BOS1</jats:italic> gene. The <jats:italic>bos1-1</jats:italic> mutation was located in chromosome 1. A T-to-A mutation in <jats:italic>BOS1</jats:italic> was identified, which changed the codon from TAC to AAC, resulting in the amino acid change from tyrosine to asparagine. <jats:italic>BOS1</jats:italic> gene encoded a grass-specific basic helix–loop–helix transcription factor, which is a novel allele of the previously cloned <jats:italic>LAX PANICLE 1</jats:italic> (<jats:italic>LAX1</jats:italic>) gene. Spatial and temporal expression profile analyses showed that <jats:italic>BOS1</jats:italic> was expressed in young panicles and was induced by phytohormones. BOS1 protein was mainly localized in the nucleus. The expression of panicle development-related genes, such as <jats:italic>OsPIN2</jats:italic>, <jats:italic>OsPIN3</jats:italic>, <jats:italic>APO1</jats:italic>, and <jats:italic>FZP</jats:italic>, was changed by <jats:italic>bos1-1</jats:italic> mutation, suggesting that the genes may be the direct or indirect targets of BOS1 to regulate panicle development. The analysis of <jats:italic>BOS1</jats:italic> genomic variation, haplotype, and haplotype network showed that <jats:italic>BOS1</jats:italic> gene had several genomic variations and haplotypes. These results laid the foundation for us to further dissect the functions of BOS1.</jats:p>

<jats:p>In domesticated apple (<jats:italic>Malus</jats:italic> x <jats:italic>domestica</jats:italic> Borkh.) and other woody perennials, floral initiation can be repressed by gibberellins (GAs). The associated mechanism is a major unanswered question in plant physiology, and understanding organismal aspects of GA signaling in apple has important commercial applications. In plants, the major mechanism for elimination of GAs and resetting of GA signaling is through catabolism by GA2-oxidases (GA2ox). We found that the GA2ox gene family in apple comprises 16 genes representing eight, clearly defined homeologous pairs, which were named as <jats:italic>MdGA2ox1A/1B</jats:italic> to <jats:italic>MdGA2ox8A/8B</jats:italic>. Expression of the genes was analyzed in the various structures of the spur, where flowers are initiated, as well as in various structures of seedlings over one diurnal cycle and in response to water-deficit and salt stress. Among the results, we found that <jats:italic>MdGA2ox2A/2B</jats:italic> dominated expression in the shoot apex and were strongly upregulated in the apex after treatment with exogenous GA<jats:sub>3</jats:sub>, suggesting potential involvement in repression of flowering. Several <jats:italic>MdGA2ox</jats:italic> genes also showed preferential expression in the leaf petiole, fruit pedicel, and the seed coat of developing seeds, potentially representing mechanisms to limit diffusion of GAs across these structures. In all contexts studied, we documented both concerted and distinct expression of individual homeologs. This work introduces an accessible woody plant model for studies of GA signaling, <jats:italic>GA2ox</jats:italic> gene regulation, and conservation/divergence of expression of homeologous genes, and should find application in development of new cultivars of apple and other tree fruits.</jats:p>

<jats:p>Wheat is one of the major cereal crop grown food worldwide and, therefore, plays has a key role in alleviating the global hunger crisis. The effects of drought stress can reduces crop yields by up to 50% globally. The use of drought-tolerant bacteria for biopriming can improve crop yields by countering the negative effects of drought stress on crop plants. Seed biopriming can reinforce the cellular defense responses to stresses via the stress memory mechanism, that its activates the antioxidant system and induces phytohormone production. In the present study, bacterial strains were isolated from rhizospheric soil taken from around the Artemisia plant at Pohang Beach, located near Daegu, in the South Korea Republic of Korea. Seventy-three isolates were screened for their growth-promoting attributes and biochemical characteristics. Among them, the bacterial strain SH-8 was selected preferred based on its plant growth-promoting bacterial traits, which are as follows: abscisic acid (ABA) concentration = 1.08 ± 0.05 ng/mL, phosphate-solubilizing index = 4.14 ± 0.30, and sucrose production = 0.61 ± 0.13 mg/mL. The novel strain SH-8 demonstrated high tolerance oxidative stress. The antioxidant analysis also showed that SH-8 contained significantly higher levels of catalase (CAT), superoxide dismutase (SOD), and ascorbic peroxidase (APX). The present study also quantified and determined the effects of biopriming wheat (Triticum aestivum) seeds with the novel strain SH-8. SH-8 was highly effective in enhancing the drought tolerance of bioprimed seeds; their drought tolerance and germination potential (GP) were increased by up to 20% and 60%, respectively, compared with those in the control group. The lowest level of impact caused by drought stress and the highest germination potential, seed vigor index (SVI), and germination energy (GE) (90%, 2160, and 80%, respectively), were recorded for seeds bioprimed with with SH-8. These results show that SH-8 enhances drought stress tolerance by up to 20%. Our study suggests that the novel rhizospheric bacterium SH-8 (gene accession number OM535901) is a valuable biostimulant that improves drought stress tolerance in wheat plants and has the potential to be used as a biofertilizer under drought conditions.</jats:p>

<jats:sec><jats:title>Introduction</jats:title><jats:p>Seeds are the most important carrier of germplasm preservation. However, an irreversible decrease in vigor can occur after the maturation of seeds, denoted as seed aging. Mitochondrion is a crucial organelle in initiation programmed cell death during seed aging. However, the underlying mechanism remains unclear.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>Our previous proteome study found that 13 mitochondria proteins underwent carbonylation modification during the aging of <jats:italic>Ulmus pumila</jats:italic> L. (Up) seeds. This study detected metal binding proteins through immobilized metal affinity chromatography (IMAC), indicating that metal binding proteins in mitochondria are the main targets of carbonization during seed aging. Biochemistry, molecular and cellular biology methods were adopted to detect metal-protein binding, protein modification and subcellular localization. Yeast and Arabidopsis were used to investigate the biological functions <jats:italic>in vivo</jats:italic>.</jats:p></jats:sec><jats:sec><jats:title>Results and discussion</jats:title><jats:p>In IMAC assay, 12 proteins were identified as Fe<jats:sup>2</jats:sup>+/Cu<jats:sup>2</jats:sup>+/Zn<jats:sup>2</jats:sup>+ binding proteins, including mitochondrial voltage dependent anion channels (VDAC). UpVDAC showed binding abilities to all the three metal ions. His204Ala (H204A) and H219A mutated UpVDAC proteins lost their metal binding ability, and became insensitive to metal-catalyzed oxidation (MCO) induced carbonylation. The overexpression of wild-type UpVDAC made yeast cells more sensitive to oxidative stress, retarded the growth of Arabidopsis seedlings and accelerated the seed aging, while overexpression of mutated UpVDAC weakened these effects of VDAC. These results reveal the relationship between the metal binding ability and carbonylation modification, as well as the probable function of VDAC in regulating cell vitality, seedling growth and seed aging.</jats:p></jats:sec>

<jats:p>Roots are the hidden parts of plants, anchoring their above-ground counterparts in the soil. They are responsible for water and nutrient uptake and for interacting with biotic and abiotic factors in the soil. The root system architecture (RSA) and its plasticity are crucial for resource acquisition and consequently correlate with plant performance while being highly dependent on the surrounding environment, such as soil properties and therefore environmental conditions. Thus, especially for crop plants and regarding agricultural challenges, it is essential to perform molecular and phenotypic analyses of the root system under conditions as near as possible to nature (#asnearaspossibletonature). To prevent root illumination during experimental procedures, which would heavily affect root development, Dark-Root (D-Root) devices (DRDs) have been developed. In this article, we describe the construction and different applications of a sustainable, affordable, flexible, and easy to assemble open-hardware bench-top LEGO® DRD, the DRD-BIBLOX (Brick Black Box). The DRD-BIBLOX consists of one or more 3D-printed rhizoboxes, which can be filled with soil while still providing root visibility. The rhizoboxes sit in a scaffold of secondhand LEGO® bricks, which allows root development in the dark and non-invasive root tracking with an infrared (IR) camera and an IR light-emitting diode (LED) cluster. Proteomic analyses confirmed significant effects of root illumination on barley root and shoot proteomes. Additionally, we confirmed the significant effect of root illumination on barley root and shoot phenotypes. Our data therefore reinforces the importance of the application of field conditions in the lab and the value of our novel device, the DRD-BIBLOX. We further provide a DRD-BIBLOX application spectrum, spanning from investigating a variety of plant species and soil conditions and simulating different environmental conditions and stresses, to proteomic and phenotypic analyses, including early root tracking in the dark.</jats:p>