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Bioinformatics investigation of the effect of volatile and non-volatile compounds of rhizobacteria in inhibiting late embryogenesis abundant protein that induces drought tolerance

  • Faegheh Etminani , Bahman Fazeli-Nasab EMAIL logo , Hittanahallikoppal Gajendramurthy Gowtham , Ali Reza Mirzaei , Jayanthi Barasarathi and Riyaz Z. Sayyed EMAIL logo
Published/Copyright: February 15, 2024
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Open Agriculture
From the journal Open Agriculture Volume 9 Issue 1

Abstract

Drought is a major problem worldwide for agriculture, horticulture, and forestry. In many cases, major physiological and biochemical changes occur due to drought stress. The plant’s response to drought stress includes a set of systems for intracellular regulation of gene expression and inter-tissue and inter-organ signaling, which ultimately leads to increased stress tolerance. Meanwhile, the role of plant growth-promoting bacteria in improving many harmful consequences of drought stress has been discussed. One of the new ways to increase tolerance to drought stress in plants is drug design using methods based on computer analysis, bioinformatics, pharmacokinetics, and molecular docking. The present study aimed to identify volatile and non-volatile compounds involved in drought tolerance using molecular docking methods. In this research, among the volatile and non-volatile compounds effective in increasing growth and inducing drought tolerance, compounds that have a high affinity for interacting with the active site of late embryogenesis abundant (LEA) protein were identified through molecular docking methods, and it was presented as a suitable inhibitor for this protein. Based on the docking results, the inhibition potentials of the studied compounds differed, and the most vital interaction in the case of LEA 3 protein was related to the gibberellic acid compound, whose energy is equivalent to −7.78 kcal/mol. Due to the basic understanding of many mechanisms operating in the interactions of plants and bacteria, it is expected that the practical use of these compounds will grow significantly in the coming years, relying on pharmacokinetic methods and molecular docking.

Keywords: computer-aided drug design; molecular docking; pharmacokinetic; virtual screening

Abbreviations

ACC

1-aminocyclopropane-1-carboxylic acid

LEA

late embryogenesis abundant protein

NCBI

Center for Biotechnology Information

PGPR

plant growth-promoting bacteria

1 Introduction

Plants normally live with different microorganisms; generally, environments rich in rhizosphere nutrients can be effective in improving the interaction between plants and microorganisms [1,2]. Despite the fact that some microorganisms might not directly contribute to the growth of plants, many beneficial bacteria do so indirectly by limiting the development of diseases and enhancing plants’ resistance to environmental challenges like salinity and drought [3,4].

Endophytes are usually defined as a group of microorganisms that live symbiotically with the plant without causing disease symptoms. Endophytes have been isolated from almost all plant tissues to date. Endophytes, most of which are fungi, have great potential for exploitation in plants. So far, only a small part of endophytes in plants have been identified. Several living and non-living factors affect the composition of endophytic communities in plants. One of the most important factors is the species of the host plant (at lower levels of the genetic pattern of the host plant) and its developmental stage, and the other is the environment in which the plant organ operates (such as soil for root endophytes); however, these effects may vary between individual ecosystems [5,6,7,8].

Plants with fungal endophytes, in addition to the ability to absorb nutrients better and grow and yield higher, are able to withstand more living and non-living stresses such as salinity, drought, and heat stress compared to plants without endophytes. Plant growth-promoting bacteria (PGPR) have the potential to enhance barley growth under drought stress [9]. The inoculation of barley plants by PGPR enhanced the indexes of plant tolerance to drought stress, such as shoot dry weight, relative water content, chlorophyll pigments content, photosynthesis efficiency (Fv/m ratio), and proline content.

Fungal endophyte species are found in most plant species living in different habitats. They can be established in root, stem, and leaf tissues and exhibit a wide range of symbionts with plants [10,11,12,13].

The coexistence of plants with microorganisms and other living organisms ensures the preservation and stability of plant species. Microbes help the absorption of water, nutrients, potassium, phosphorus, and nitrogen of the plant, and as a result, the biomass and growth of the plant have increased in harsh environmental conditions. Various morphological, biochemical, physiological, molecular, and ecological traits and processes of the plants are impaired under drought stress conditions. Different key factors such as growth stages, age, plant species, and drought severity and duration affect the plant responses to drought [14].

Considering the importance of the symbiosis of effective fungi in the growth of plants and their interaction with mineral elements of the soil, these symbiotic fungi can be effective in the development programs of medicinal plant cultivation [15,16,17,18,19].

Research on endophytic communities in the host has shown that, in general, lots of fungal species can be separated from plant tissues after surface sterilization [20]. In all investigated plant species, in general, the pattern of endophytic communities is directly related to the geographical distribution pattern of their host plant species [21]. For example, endophytic communities are similar in host plant species growing in the same location. But there are significant differences in the abundance and distribution of fungal species in various plant tissues that serve as the host. The abundance and spread of fungal endophyte species may also be influenced by the host plant’s age [22]. A higher colonization rate of endophytic fungi can be observed in homogeneous stations with a closed canopy. There may be a correlation between altitude and wet climate with endophyte populations [23]. The population of endophytes varies from species to species and from plant to plant [24]. They can promote plant growth and enhance their resistance toward various pathogens and environmental stresses [25].

In the same species, the endophyte population, in addition to being unique from one region to another, also varies with changing climatic conditions in the same region [24]. Researchers have tried to clarify the molecular mechanisms effective in creating endophyte communities in plants; but very limited information is available in this field [26]. There is evidence that shade, compared to light, increased endophyte density in the leaf tissue of six grass species [27]. As we know, the biodiversity of organisms does not have a uniform distribution, and their distribution in different regions is very different [28,29].

PGPR are useful bacteria that can increase plant growth by producing volatile organic compounds (VOCs) and increasing plant tolerance to environmental stresses [30,31,32]. Some of these PGPR are used in agriculture to improve plant growth, increase yield, and improve disease resistance. By creating non-volatile growth-stimulating substances, including auxin and cytokinin hormones, as well as ACC deaminase (which lowers the level of ethylene) and siderophore, PGPR can effectively aid in the absorption of nutrients by plants [33,34,35].

Although volatile compounds of PGPR do not specifically include plant growth hormones or siderophores. However, the role of volatile compounds in the regulation of endogenous auxin homeostasis has been reported in various studies [36,37]. In addition to volatile compounds in plant growth, they are effective in inducing resistance against pathogens and abiotic stresses [38]. Some VOCs like 2,3-butanediol can induce resistance to Erwinia carotovora subsp. carotovora [39]. Tridecane produced by Paenibacillus polymyxa E681 induced systematic resistance in plants [40]. 3-Pentanol and 2-butanone were reported effective against Pseudomonas syringae pv. Lachrymans [41].

Some review studies have been published on the chemical makeup of volatile compounds and their significance in promoting pathogen resistance, increasing biomass, and reducing the effects of abiotic stresses like salt stress and drought stress as a result of researchers’ growing interest in the study of volatile compounds [42,43,44,45,46].

One of the most significant obstacles restricting plant growth, particularly in dry environments, is water. So that each year, drought stress lowers the yield of several items [47]. Dehydration is one of the most common threats that plants face during osmotic stress caused by salinity, drought, or cold. Accumulation of osmo-protecting compounds in plants increases the osmotic pressure of cells to prevent its loss by reducing the amount of free water in cells and helping the stability of protein and membrane structure. In the conditions of osmotic stress, in Arabidopsis plants that were exposed to GB03 volatile compounds, higher amounts of choline and glycine betaine were observed in the plants compared to the control treatment [48,49,50]. Choline and glycine betaine play an important role in the tolerance of plants to drought stress [51,52]. Volatile compounds increase PEAMT transcript [53,54].

In the late 1980s, studies and investigations made it clear that molecular mechanisms are among the most important genetic processes (including DNA replication, transcription, translation, and even gene regulation). The need for gene expression is controlled by the environment in which it grows, and if there is no need for the gene product, that gene will remain silent and inactive. By using bioinformatics to analyze biological data, it is possible to anticipate the structure and function of gene products, determine the evolutionary link between genes and protein sequences, and align sequences in databases to find gene similarities and differences [55,56,57].

Drought is one of the important environmental limiting factors that affects the production and performance of crops in many arid and semi-arid regions. Drought resistance is a complex trait whose occurrence depends on the action and reaction between different physiological and biochemical traits. A large group of stress-regulated genes has been discovered by testing embryos that are naturally desiccated during seed maturation. These genes are anticipated to produce late embryogenesis abundant (LEA) proteins, which are thought to help defend the cell membrane. In addition to the plant kingdom, LEA proteins have also been found in various animals and microbes. They are a huge and diversified family. Hydrophilic amino acids, low molecular weight LEA proteins, and disordered saccharides with repetitive motifs are all characteristics of LEA proteins in their native state. Based on main and homologous sequences, LEA proteins are divided into eight families in the Pfam database: LEA-1, LEA-2, LEA-3, LEA-4, LEA-5, LEA-6, PVLEA-18, and SMPO [58,59,60,61,62].

Considering the unknown mechanism of induction of resistance by LEA proteins, studying the structural and functional domains of these proteins in drought-resistant and sensitive species and examining the differences between them provide a window to identify the mechanism and induction of resistance by these proteins and the transfer of relevant genes through genetic engineering [63].

Today, one of the new ways to increase tolerance to drought stress in plants is drug design using methods based on computer calculations and bioinformatics [64,65]. Using computational methods, it is possible to check the interaction of chemical compounds with proteins before conducting experimental tests, and after determining the compounds that are most likely to bind to the target, they can be checked in the laboratory and living systems. Molecular docking examines the level of molecular interaction between ligands and receptors [66,67]. Docking is usually used to assess the binding interaction of small molecule candidates to their protein targets to anticipate the preference and function of ligands. Molecular docking illustrates how two or more molecules communicate with each other [68]. This technique can be used to investigate the inhibitory effect of natural compounds against special targets [69].

In this research, among the volatile and non-volatile compounds that are effective in increasing growth and inducing drought tolerance, compounds that have high affinity in interaction with the active site of LEA are identified through molecular docking methods and will be suggested as suitable inhibitors for this protein.

2 Materials and methods

2.1 Phylogenetic analysis of the studied protein sequence using the software

First, the protein sequence of LEA 3 [70,71] was studied through comparison with similar sequences in other plants from the NCBI website. Alignment of protein sequences with the sequences of type strains was done using Clustal W software [72]. Phylogenetic analyses were performed by the neighbor-joining (NJ) method [73] with the help of Mega 6 software [74].

2.2 Obtaining and improving the LEA 3 protein’s three-dimensional structure

The three-dimensional structure model of LEA 3 protein was obtained using the I-TASSER server. Then, using http://sysbio.rnet.missouri.edu/3Drefine, their structure was optimized. The Ramachandran diagram was used to depict the bond angles in terms of energy level and stability in terms of phi and psi angles of the mentioned proteins. These models were visualized by Chimera 1.8 software [75,76].

2.3 Preparing volatile chemicals and examining their physical characteristics

The PubChem chemical and medicinal substance database [77], located at pubchem.ncbi.nlm.nih.gov, was used to obtain the structures of the volatile and non-volatile molecules produced by bacteria. Python Viewer 1.5 software was used to convert a file pertaining to the three-dimensional structure of chemical compounds from SDF to PDB format, separate the ligand from the protein structure, add polar hydrogen, examine the placement of ligands in the active site, and determine the surface charge of the aforementioned structures.

Before investigating the interaction between ligand and protein, the intended compounds were investigated in terms of physicochemical properties and non-toxicity. Solubility, molecular weight, Log Po/w Log S (ESOL), and the ability to inhibit five important cytochromes including CYP2C19 (Cytochrome P450 2C19), CYP3A4 (Cytochrome P450 3A4), CYP2D6 (Cytochrome P450 2D6), CYP2C9 (Cytochrome P450 2C9), and CYP1A2 (Cytochrome P450 1A2) as genotoxicity and cytotoxicity were evaluated using the SwissADME online server at http://www.swissadme.ch. Only substances that met the criteria for the aforementioned indicators were chosen. This server is online software that provides the possibility of predicting physicochemical properties and cytotoxicity by receiving chemical molecule information in the form of mol or SMILE files. The quantity LogP (logarithm of the partition coefficient of octanol/water) is the amount of solubility in water and fat (it is used to predict the amount of solubility). Then, using Avogadro software (http://avogadro.cc), all of the volatile and non-volatile substances made by bacteria and proteins were tuned to check interactions in the most stable state possible in terms of energy and structure and to prevent false positive and negative results.

2.4 Molecular docking

It appears to be required to forecast and create protein inhibitor molecules involved in drought stress using quick computational algorithms and tools like molecular docking. Therefore, in this research, to investigate the effect of volatile compounds on LEA 3 protein involved in drought resistance, molecular docking between bacterial volatile compounds and LEA 3 protein was carried out. This work was done using specialized software autogrid4.2.6 and autodock4.2.6 (version 2014). For inhibitor docking, a box size of 60 × 60 × 60 was chosen. To search the conformational space of molecules, the AutoDock-4.2.6 software’s Lamarckian genetic algorithm was employed. Finally, AutodockTools and Ligplot tools were used to examine the outcomes [78].

3 Results

The three-dimensional structure of the LEA 3 protein, which was designed using the ILTASSER bioinformatics tool, is shown in Figure 1. Also, the results related to the evaluation of these models are given in Table 1. The phylogenetic tree of the LEA 3 protein sequence studied in the research is given in Figure 2.

Figure 1 3D structure of LEA 3 protein in Arabidopsis plant. C-score = −3.58. Estimated TM-score = 0.32 ± 0.11. Estimated RMSD = 11.8 ± 4.5 Å.
Figure 1

3D structure of LEA 3 protein in Arabidopsis plant. C-score = −3.58. Estimated TM-score = 0.32 ± 0.11. Estimated RMSD = 11.8 ± 4.5 Å.

Table 1

Comparison of Ramachandran plot statistics of LEA 3 model

Model evaluation
Number of residues in Favored region 55.7%
Allowed region 27.8%
Residues in Generously allowed region 7.6%
Disallowed region 8.9%
Figure 2 NJ tree derived from LEA 3 sequences in MEGA6.0 that are linked. The proportion of the bootstrap value derived from 1,000 samples is represented by the number of nodes. The substitutions per amino acid position are shown by the bar at 0.02.
Figure 2

NJ tree derived from LEA 3 sequences in MEGA6.0 that are linked. The proportion of the bootstrap value derived from 1,000 samples is represented by the number of nodes. The substitutions per amino acid position are shown by the bar at 0.02.

The B-factor is a measure of how thermally mobile residues and atoms are naturally in proteins. With the use of template proteins from the PDB and the sequence profiles generated by sequence databases, I-TASSER infers this value. According to B = (B′ − u)/s, where B′ is the raw B-factor value and u and s are the mean and standard deviation of the raw B-factors throughout the sequence, respectively, the B-factor profile presented corresponds to the normalized B-factor of the target protein (Figure 3).

Figure 3 Normalized B-factor plot of LEA 3 protein.
Figure 3

Normalized B-factor plot of LEA 3 protein.

Ramachandran’s diagram related to LEA 3 protein was determined to determine the energy level and stability in terms of two angles φ and ψ in proteins (Figure 4) (Table 1). The Ramachandran plot indicates that for the given protein, residues belong to the most favored regions (55.7%), additionally allowed regions (27.8%), generously allowed regions (7.6%), and disallowed regions (8.9%).

Figure 4 Ramachandran plot of the LEA 3 model.
Figure 4

Ramachandran plot of the LEA 3 model.

For this protein, 14 residues, that is, Proline 58, Isoleucine 85, Alanine 84, Leucine 36, Asparagine 21, Alanine 52, Aspartic acid 37, Alanine, SER 27, Arginine 26, Valine 23, Leucine 82, Aspartic acid 78, and Phenylalanine 28 belong to generously allowed regions and disallowed regions.

The examined volatile compounds’ physicochemical characteristics, such as their three-dimensional structure, the quantity of hydrogen bond donors and acceptors, and their potential toxicity, were identified (Table S1).

The results of predicting the physicochemical properties and toxicity potential of the volatile compounds produced from the studied PGPR are shown in Table S2.

3.1 Molecular docking

The results are displayed in the supplementary file. The data pertaining to changes in binding energy and ligand interactions, including hydrogen bonds and hydrophobic interactions, were recorded, and the binding energy was estimated for each combination (Table S3).

The inhibitory potential of the investigated substances varies according to the docking results. In the instance of the LEA 3 protein, gibberellic acid, whose energy is equal to −7.78 kcal/mol, is the source of the strongest interaction. Binding energy is a measure of how strongly molecules bind to the protein’s active site. The most significant amino acids that this protein interacts with include Tyr 68, Arg 48, Ala 35, Gln 11, Glu 44, Phe 14, Gly 15, Leu 36, Thr 34, Met 45, Glu 17, Lys 18, and Glu 17 (Figure 5).

Figure 5 The most important amino acids involved in the reaction.
Figure 5

The most important amino acids involved in the reaction.

4 Discussion

Plant growth-stimulating bacteria are essential in plant nutrition and health, especially in the production of healthy and organic products. Bacteria stimulate growth and development through chemical messengers, including flowering, germination, senescence, and various reactions to stress. Bacteria in the rhizosphere are greatly influenced by plant roots. Rhizosphere bacteria are useful, harmful, or ineffective in terms of the type of effect they can have on the plant [79,80,81,82]. Beneficial and non-symbiotic rhizosphere bacteria (PGPR) can directly or indirectly increase plant growth by one or more specific mechanisms. Volatile and non-volatile bacteria include a wide range of PGPR, including Pseudomonas, Bacillus, Azospirillum, Flavobacterium, and Azotobacter. Considering the wide range of PGPR, the variety of target plants, and the multiplicity of their impact mechanisms, the distribution of these bacteria is different in soil and climatic conditions [83,84,85,86,87].

More than 80% of the plant species, from bryophytes to tracheophytes, are symbiotic with mycorrhizal fungi, a heterogeneous group of several fungal species [88]. This association, which is thought to have developed around 460 million years ago, was crucial in the emergence of plants on Earth [89]. Only roughly 240 species have been reported based on morphology in the Glomeromycota branch, despite the prevalence of these fungus and the diversity of their relationships with plant species [90,91]. Because the mushroom community with the plant is a mutually beneficial event that provides the plant with the carbon of the fungus, and the fungi help the plant absorb phosphate and other minerals from the soil. As a result of this symbiosis, the increase of plant biomass and the resistance of the plant to stresses and pathogens are strengthened [92]. This coexistence is important for the development of production and productivity of important agricultural, nutritional, and medicinal products [93].

The identification of the soil microbiome has had a significant impact on how well the ecosystem functions as well as on crop productivity without having any negative consequences on the environment. Analysis and research into the intricate microbial populations in soil are therefore crucial. On the other hand, microbial secondary metabolites are essential for agricultural applications and drug discovery. The wide family of varied substances known as plant hormones is likewise produced by bacteria. These hormones are broken down into many structural classes [94,95,96,97]. For instance, lipid-based compounds, terpenoid carboxylic acids, plant steroids, derivatives of purines and indoles, and so forth. All hormones share the trait of typically being in tissues at specific concentrations [98,99,100]. As it was said, one of the new ways to increase tolerance to drought stress in plants is drug design using methods based on bioinformatics analysis, pharmacokinetics, and molecular docking [101]. The results of this research showed that the volatile and non-volatile compounds effective in increasing growth and inducing drought tolerance, in interaction with the active site of LEA protein, had different inhibitory potentials, which shows that LEA proteins have an unknown function [102,103,104,105].

LEA proteins may contribute to drought resilience, according to a substantial body of research. The protection of cell structures from the effects of water loss by water retention, sequestration of ions, and direct protection of other proteins or membranes are some of the various mechanisms that have been suggested to achieve this goal [106,107]. There is proof that LEA proteins, despite being different, could be related. Additionally, overlapping sets with a focus on alpha-helical structure and, on a wider scale, filaments show this link, all of which are in strong accord with experimental data. Under stress, LEA proteins are probably going to help chaperones in the nucleus, along with the cytoskeleton and through their function in DNA binding. Determining the function and method of action of non-globular, low-complexity proteins, such as LEA proteins, can be particularly difficult. To be able to adequately evaluate such proteins, new tools and tool combinations are required as opposed to masking and disregarding low complexity domains. Due to the basic understanding of many mechanisms operating in the interactions of plants and bacteria, it is expected that the practical use of these compounds will grow significantly in the coming years, relying on pharmacokinetic methods and molecular docking.

  1. Funding information: The authors state no funding involved.

  2. Conflict of interest: The authors state no conflict of interest.

  3. Data availability statement: All data generated or analyzed during this study are included in this published article and its supplementary information file.

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Received: 2023-08-15
Revised: 2023-10-16
Accepted: 2024-01-03
Published Online: 2024-02-15

© 2024 the author(s), published by De Gruyter

This work is licensed under the Creative Commons Attribution 4.0 International License.

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  74. Chemometrics for mapping the spatial nitrate distribution on the leaf lamina of fenugreek grown under varying nitrogenous fertilizer doses
  75. Pomegranate peel ethanolic extract: A promising natural antioxidant, antimicrobial agent, and novel approach to mitigate rancidity in used edible oils
  76. Transformative learning and engagement with organic farming: Lessons learned from Indonesia
  77. Tourism in rural areas as a broader concept: Some insights from the Portuguese reality
  78. Assessment enhancing drought tolerance in henna (Lawsonia inermis L.) ecotypes through sodium nitroprusside foliar application
  79. Edible insects: A survey about perceptions regarding possible beneficial health effects and safety concerns among adult citizens from Portugal and Romania
  80. Phenological stages analysis in peach trees using electronic nose
  81. Harvest date and salicylic acid impact on peanut (Arachis hypogaea L.) properties under different humidity conditions
  82. Hibiscus sabdariffa L. petal biomass: A green source of nanoparticles of multifarious potential
  83. Use of different vegetation indices for the evaluation of the kinetics of the cherry tomato (Solanum lycopersicum var. cerasiforme) growth based on multispectral images by UAV
  84. First evidence of microplastic pollution in mangrove sediments and its ingestion by coral reef fish: Case study in Biawak Island, Indonesia
  85. Physical and textural properties and sensory acceptability of wheat bread partially incorporated with unripe non-commercial banana cultivars
  86. Cereibacter sphaeroides ST16 and ST26 were used to solubilize insoluble P forms to improve P uptake, growth, and yield of rice in acidic and extreme saline soil
  87. Avocado peel by-product in cattle diets and supplementation with oregano oil and effects on production, carcass, and meat quality
  88. Optimizing inorganic blended fertilizer application for the maximum grain yield and profitability of bread wheat and food barley in Dawuro Zone, Southwest Ethiopia
  89. The acceptance of social media as a channel of communication and livestock information for sheep farmers
  90. Adaptation of rice farmers to aging in Thailand
  91. Combined use of improved maize hybrids and nitrogen application increases grain yield of maize, under natural Striga hermonthica infestation
  92. From aquatic to terrestrial: An examination of plant diversity and ecological shifts
  93. Statistical modelling of a tractor tractive performance during ploughing operation on a tropical Alfisol
  94. Participation in artisanal diamond mining and food security: A case study of Kasai Oriental in DR Congo
  95. Assessment and multi-scenario simulation of ecosystem service values in Southwest China’s mountainous and hilly region
  96. Analysis of agricultural emissions and economic growth in Europe in search of ecological balance
  97. Bacillus thuringiensis strains with high insecticidal activity against insect larvae of the orders Coleoptera and Lepidoptera
  98. Technical efficiency of sugarcane farming in East Java, Indonesia: A bootstrap data envelopment analysis
  99. Comparison between mycobiota diversity and fungi and mycotoxin contamination of maize and wheat
  100. Evaluation of cultivation technology package and corn variety based on agronomy characters and leaf green indices
  101. Exploring the association between the consumption of beverages, fast foods, sweets, fats, and oils and the risk of gastric and pancreatic cancers: Findings from case–control study
  102. Phytochemical composition and insecticidal activity of Acokanthera oblongifolia (Hochst.) Benth & Hook.f. ex B.D.Jacks. extract on life span and biological aspects of Spodoptera littoralis (Biosd.)
  103. Land use management solutions in response to climate change: Case study in the central coastal areas of Vietnam
  104. Evaluation of coffee pulp as a feed ingredient for ruminants: A meta-analysis
  105. Interannual variations of normalized difference vegetation index and potential evapotranspiration and their relationship in the Baghdad area
  106. Harnessing synthetic microbial communities with nitrogen-fixing activity to promote rice growth
  107. Agronomic and economic benefits of rice–sweetpotato rotation in lowland rice cropping systems in Uganda
  108. Response of potato tuber as an effect of the N-fertilizer and paclobutrazol application in medium altitude
  109. Bridging the gap: The role of geographic proximity in enhancing seed sustainability in Bandung District
  110. Evaluation of Abrams curve in agricultural sector using the NARDL approach
  111. Challenges and opportunities for young farmers in the implementation of the Rural Development Program 2014–2020 of the Republic of Croatia
  112. Yield stability of ten common bean (Phaseolus vulgaris L.) genotypes at different sowing dates in Lubumbashi, South-East of DR Congo
  113. Effects of encapsulation and combining probiotics with different nitrate forms on methane emission and in vitro rumen fermentation characteristics
  114. Phytochemical analysis of Bienertia sinuspersici extract and its antioxidant and antimicrobial activities
  115. Evaluation of relative drought tolerance of grapevines by leaf fluorescence parameters
  116. Yield assessment of new streak-resistant topcross maize hybrids in Benin
  117. Improvement of cocoa powder properties through ultrasonic- and microwave-assisted alkalization
  118. Potential of ecoenzymes made from nutmeg (Myristica fragrans) leaf and pulp waste as bioinsecticides for Periplaneta americana
  119. Analysis of farm performance to realize the sustainability of organic cabbage vegetable farming in Getasan Semarang, Indonesia
  120. Revealing the influences of organic amendment-derived dissolved organic matter on growth and nutrient accumulation in lettuce seedlings (Lactuca sativa L.)
  121. Identification of viruses infecting sweetpotato (Ipomoea batatas Lam.) in Benin
  122. Assessing the soil physical and chemical properties of long-term pomelo orchard based on tree growth
  123. Investigating access and use of digital tools for agriculture among rural farmers: A case study of Nkomazi Municipality, South Africa
  124. Does sex influence the impact of dietary vitD3 and UVB light on performance parameters and welfare indicators of broilers?
  125. Design of intelligent sprayer control for an autonomous farming drone using a multiclass support vector machine
  126. Deciphering salt-responsive NB-ARC genes in rice transcriptomic data: A bioinformatics approach with gene expression validation
  127. Review Articles
  128. Impact of nematode infestation in livestock production and the role of natural feed additives – A review
  129. Role of dietary fats in reproductive, health, and nutritional benefits in farm animals: A review
  130. Climate change and adaptive strategies on viticulture (Vitis spp.)
  131. The false tiger of almond, Monosteira unicostata (Hemiptera: Tingidae): Biology, ecology, and control methods
  132. A systematic review on potential analogy of phytobiomass and soil carbon evaluation methods: Ethiopia insights
  133. A review of storage temperature and relative humidity effects on shelf life and quality of mango (Mangifera indica L.) fruit and implications for nutrition insecurity in Ethiopia
  134. Green extraction of nutmeg (Myristica fragrans) phytochemicals: Prospective strategies and roadblocks
  135. Potential influence of nitrogen fertilizer rates on yield and yield components of carrot (Dacus carota L.) in Ethiopia: Systematic review
  136. Corn silk: A promising source of antimicrobial compounds for health and wellness
  137. State and contours of research on roselle (Hibiscus sabdariffa L.) in Africa
  138. The potential of phosphorus-solubilizing purple nonsulfur bacteria in agriculture: Present and future perspectives
  139. Minor millets: Processing techniques and their nutritional and health benefits
  140. Meta-analysis of reproductive performance of improved dairy cattle under Ethiopian environmental conditions
  141. Review on enhancing the efficiency of fertilizer utilization: Strategies for optimal nutrient management
  142. The nutritional, phytochemical composition, and utilisation of different parts of maize: A comparative analysis
  143. Motivations for farmers’ participation in agri-environmental scheme in the EU, literature review
  144. Evolution of climate-smart agriculture research: A science mapping exploration and network analysis
  145. Short Communications
  146. Music enrichment improves the behavior and leukocyte profile of dairy cattle
  147. Effect of pruning height and organic fertilization on the morphological and productive characteristics of Moringa oleifera Lam. in the Peruvian dry tropics
  148. Corrigendum
  149. Corrigendum to “Bioinformatics investigation of the effect of volatile and non-volatile compounds of rhizobacteria in inhibiting late embryogenesis abundant protein that induces drought tolerance”
  150. Corrigendum to “Composition and quality of winter annual agrestal and ruderal herbages of two different land-use types”
  151. Special issue: Smart Agriculture System for Sustainable Development: Methods and Practices
  152. Construction of a sustainable model to predict the moisture content of porang powder (Amorphophallus oncophyllus) based on pointed-scan visible near-infrared spectroscopy
  153. FruitVision: A deep learning based automatic fruit grading system
  154. Energy harvesting and ANFIS modeling of a PVDF/GO-ZNO piezoelectric nanogenerator on a UAV
  155. Effects of stress hormones on digestibility and performance in cattle: A review
  156. Special Issue of The 4th International Conference on Food Science and Engineering (ICFSE) 2022 - Part II
  157. Assessment of omega-3 and omega-6 fatty acid profiles and ratio of omega-6/omega-3 of white eggs produced by laying hens fed diets enriched with omega-3 rich vegetable oil
  158. Special Issue on FCEM - International Web Conference on Food Choice & Eating Motivation - Part II
  159. Special Issue on FCEM – International Web Conference on Food Choice & Eating Motivation: Message from the editor
  160. Fruit and vegetable consumption: Study involving Portuguese and French consumers
  161. Knowledge about consumption of milk: Study involving consumers from two European Countries – France and Portugal
https://doi.org/10.1515/opag-2022-0252
Keywords for this article
computer-aided drug design; molecular docking; pharmacokinetic; virtual screening
Creative Commons
BY 4.0

Articles in the same Issue

  1. Regular Articles
  2. Supplementation of P-solubilizing purple nonsulfur bacteria, Rhodopseudomonas palustris improved soil fertility, P nutrient, growth, and yield of Cucumis melo L.
  3. Yield gap variation in rice cultivation in Indonesia
  4. Effects of co-inoculation of indole-3-acetic acid- and ammonia-producing bacteria on plant growth and nutrition, soil elements, and the relationships of soil microbiomes with soil physicochemical parameters
  5. Impact of mulching and planting time on spring-wheat (Triticum aestivum) growth: A combined field experiment and empirical modeling approach
  6. Morphological diversity, correlation studies, and multiple-traits selection for yield and yield components of local cowpea varieties
  7. Participatory on-farm evaluation of new orange-fleshed sweetpotato varieties in Southern Ethiopia
  8. Yield performance and stability analysis of three cultivars of Gayo Arabica coffee across six different environments
  9. Biology of Spodoptera frugiperda (Lepidoptera: Noctuidae) on different types of plants feeds: Potency as a pest on various agricultural plants
  10. Antidiabetic activity of methanolic extract of Hibiscus sabdariffa Linn. fruit in alloxan-induced Swiss albino diabetic mice
  11. Bioinformatics investigation of the effect of volatile and non-volatile compounds of rhizobacteria in inhibiting late embryogenesis abundant protein that induces drought tolerance
  12. Nicotinamide as a biostimulant improves soybean growth and yield
  13. Farmer’s willingness to accept the sustainable zoning-based organic farming development plan: A lesson from Sleman District, Indonesia
  14. Uncovering hidden determinants of millennial farmers’ intentions in running conservation agriculture: An application of the Norm Activation Model
  15. Mediating role of leadership and group capital between human capital component and sustainability of horticultural agribusiness institutions in Indonesia
  16. Biochar technology to increase cassava crop productivity: A study of sustainable agriculture on degraded land
  17. Effect of struvite on the growth of green beans on Mars and Moon regolith simulants
  18. UrbanAgriKG: A knowledge graph on urban agriculture and its embeddings
  19. Provision of loans and credit by cocoa buyers under non-price competition: Cocoa beans market in Ghana
  20. Effectiveness of micro-dosing of lime on selected chemical properties of soil in Banja District, North West, Ethiopia
  21. Effect of weather, nitrogen fertilizer, and biostimulators on the root size and yield components of Hordeum vulgare
  22. Effects of selected biostimulants on qualitative and quantitative parameters of nine cultivars of the genus Capsicum spp.
  23. Growth, yield, and secondary metabolite responses of three shallot cultivars at different watering intervals
  24. Design of drainage channel for effective use of land on fully mechanized sugarcane plantations: A case study at Bone Sugarcane Plantation
  25. Technical feasibility and economic benefit of combined shallot seedlings techniques in Indonesia
  26. Control of Meloidogyne javanica in banana by endophytic bacteria
  27. Comparison of important quality components of red-flesh kiwifruit (Actinidia chinensis) in different locations
  28. Efficiency of rice farming in flood-prone areas of East Java, Indonesia
  29. Comparative analysis of alpine agritourism in Trentino, Tyrol, and South Tyrol: Regional variations and prospects
  30. Detection of Fusarium spp. infection in potato (Solanum tuberosum L.) during postharvest storage through visible–near-infrared and shortwave–near-infrared reflectance spectroscopy
  31. Forage yield, seed, and forage qualitative traits evaluation by determining the optimal forage harvesting stage in dual-purpose cultivation in safflower varieties (Carthamus tinctorius L.)
  32. The influence of tourism on the development of urban space: Comparison in Hanoi, Danang, and Ho Chi Minh City
  33. Optimum intra-row spacing and clove size for the economical production of garlic (Allium sativum L.) in Northwestern Highlands of Ethiopia
  34. The role of organic rice farm income on farmer household welfare: Evidence from Yogyakarta, Indonesia
  35. Exploring innovative food in a developing country: Edible insects as a sustainable option
  36. Genotype by environment interaction and performance stability of common bean (Phaseolus vulgaris L.) cultivars grown in Dawuro zone, Southwestern Ethiopia
  37. Factors influencing green, environmentally-friendly consumer behaviour
  38. Factors affecting coffee farmers’ access to financial institutions: The case of Bandung Regency, Indonesia
  39. Morphological and yield trait-based evaluation and selection of chili (Capsicum annuum L.) genotypes suitable for both summer and winter seasons
  40. Sustainability analysis and decision-making strategy for swamp buffalo (Bubalus bubalis carabauesis) conservation in Jambi Province, Indonesia
  41. Understanding factors affecting rice purchasing decisions in Indonesia: Does rice brand matter?
  42. An implementation of an extended theory of planned behavior to investigate consumer behavior on hygiene sanitation-certified livestock food products
  43. Information technology adoption in Indonesia’s small-scale dairy farms
  44. Draft genome of a biological control agent against Bipolaris sorokiniana, the causal phytopathogen of spot blotch in wheat (Triticum turgidum L. subsp. durum): Bacillus inaquosorum TSO22
  45. Assessment of the recurrent mutagenesis efficacy of sesame crosses followed by isolation and evaluation of promising genetic resources for use in future breeding programs
  46. Fostering cocoa industry resilience: A collaborative approach to managing farm gate price fluctuations in West Sulawesi, Indonesia
  47. Field investigation of component failures for selected farm machinery used in small rice farming operations
  48. Near-infrared technology in agriculture: Rapid, simultaneous, and non-destructive determination of inner quality parameters on intact coffee beans
  49. The synergistic application of sucrose and various LED light exposures to enhance the in vitro growth of Stevia rebaudiana (Bertoni)
  50. Weather index-based agricultural insurance for flower farmers: Willingness to pay, sales, and profitability perspectives
  51. Meta-analysis of dietary Bacillus spp. on serum biochemical and antioxidant status and egg quality of laying hens
  52. Biochemical characterization of trypsin from Indonesian skipjack tuna (Katsuwonus pelamis) viscera
  53. Determination of C-factor for conventional cultivation and soil conservation technique used in hop gardens
  54. Empowering farmers: Unveiling the economic impacts of contract farming on red chilli farmers’ income in Magelang District, Indonesia
  55. Evaluating salt tolerance in fodder crops: A field experiment in the dry land
  56. Labor productivity of lowland rice (Oryza sativa L.) farmers in Central Java Province, Indonesia
  57. Cropping systems and production assessment in southern Myanmar: Informing strategic interventions
  58. The effect of biostimulants and red mud on the growth and yield of shallots in post-unlicensed gold mining soil
  59. Effects of dietary Adansonia digitata L. (baobab) seed meal on growth performance and carcass characteristics of broiler chickens: A systematic review and meta-analysis
  60. Analysis and structural characterization of the vid-pisco market
  61. Pseudomonas fluorescens SP007s enhances defense responses against the soybean bacterial pustule caused by Xanthomonas axonopodis pv. glycines
  62. A brief investigation on the prospective of co-composted biochar as a fertilizer for Zucchini plants cultivated in arid sandy soil
  63. Supply chain efficiency of red chilies in the production center of Sleman Indonesia based on performance measurement system
  64. Investment development path for developed economies: Is agriculture different?
  65. Power relations among actors in laying hen business in Indonesia: A MACTOR analysis
  66. High-throughput digital imaging and detection of morpho-physiological traits in tomato plants under drought
  67. Converting compression ignition engine to dual-fuel (diesel + CNG) engine and experimentally investigating its performance and emissions
  68. Structuration, risk management, and institutional dynamics in resolving palm oil conflicts
  69. Spacing strategies for enhancing drought resilience and yield in maize agriculture
  70. Composition and quality of winter annual agrestal and ruderal herbages of two different land-use types
  71. Investigating Spodoptera spp. diversity, percentage of attack, and control strategies in the West Java, Indonesia, corn cultivation
  72. Yield stability of biofertilizer treatments to soybean in the rainy season based on the GGE biplot
  73. Evaluating agricultural yield and economic implications of varied irrigation depths on maize yield in semi-arid environments, at Birfarm, Upper Blue Nile, Ethiopia
  74. Chemometrics for mapping the spatial nitrate distribution on the leaf lamina of fenugreek grown under varying nitrogenous fertilizer doses
  75. Pomegranate peel ethanolic extract: A promising natural antioxidant, antimicrobial agent, and novel approach to mitigate rancidity in used edible oils
  76. Transformative learning and engagement with organic farming: Lessons learned from Indonesia
  77. Tourism in rural areas as a broader concept: Some insights from the Portuguese reality
  78. Assessment enhancing drought tolerance in henna (Lawsonia inermis L.) ecotypes through sodium nitroprusside foliar application
  79. Edible insects: A survey about perceptions regarding possible beneficial health effects and safety concerns among adult citizens from Portugal and Romania
  80. Phenological stages analysis in peach trees using electronic nose
  81. Harvest date and salicylic acid impact on peanut (Arachis hypogaea L.) properties under different humidity conditions
  82. Hibiscus sabdariffa L. petal biomass: A green source of nanoparticles of multifarious potential
  83. Use of different vegetation indices for the evaluation of the kinetics of the cherry tomato (Solanum lycopersicum var. cerasiforme) growth based on multispectral images by UAV
  84. First evidence of microplastic pollution in mangrove sediments and its ingestion by coral reef fish: Case study in Biawak Island, Indonesia
  85. Physical and textural properties and sensory acceptability of wheat bread partially incorporated with unripe non-commercial banana cultivars
  86. Cereibacter sphaeroides ST16 and ST26 were used to solubilize insoluble P forms to improve P uptake, growth, and yield of rice in acidic and extreme saline soil
  87. Avocado peel by-product in cattle diets and supplementation with oregano oil and effects on production, carcass, and meat quality
  88. Optimizing inorganic blended fertilizer application for the maximum grain yield and profitability of bread wheat and food barley in Dawuro Zone, Southwest Ethiopia
  89. The acceptance of social media as a channel of communication and livestock information for sheep farmers
  90. Adaptation of rice farmers to aging in Thailand
  91. Combined use of improved maize hybrids and nitrogen application increases grain yield of maize, under natural Striga hermonthica infestation
  92. From aquatic to terrestrial: An examination of plant diversity and ecological shifts
  93. Statistical modelling of a tractor tractive performance during ploughing operation on a tropical Alfisol
  94. Participation in artisanal diamond mining and food security: A case study of Kasai Oriental in DR Congo
  95. Assessment and multi-scenario simulation of ecosystem service values in Southwest China’s mountainous and hilly region
  96. Analysis of agricultural emissions and economic growth in Europe in search of ecological balance
  97. Bacillus thuringiensis strains with high insecticidal activity against insect larvae of the orders Coleoptera and Lepidoptera
  98. Technical efficiency of sugarcane farming in East Java, Indonesia: A bootstrap data envelopment analysis
  99. Comparison between mycobiota diversity and fungi and mycotoxin contamination of maize and wheat
  100. Evaluation of cultivation technology package and corn variety based on agronomy characters and leaf green indices
  101. Exploring the association between the consumption of beverages, fast foods, sweets, fats, and oils and the risk of gastric and pancreatic cancers: Findings from case–control study
  102. Phytochemical composition and insecticidal activity of Acokanthera oblongifolia (Hochst.) Benth & Hook.f. ex B.D.Jacks. extract on life span and biological aspects of Spodoptera littoralis (Biosd.)
  103. Land use management solutions in response to climate change: Case study in the central coastal areas of Vietnam
  104. Evaluation of coffee pulp as a feed ingredient for ruminants: A meta-analysis
  105. Interannual variations of normalized difference vegetation index and potential evapotranspiration and their relationship in the Baghdad area
  106. Harnessing synthetic microbial communities with nitrogen-fixing activity to promote rice growth
  107. Agronomic and economic benefits of rice–sweetpotato rotation in lowland rice cropping systems in Uganda
  108. Response of potato tuber as an effect of the N-fertilizer and paclobutrazol application in medium altitude
  109. Bridging the gap: The role of geographic proximity in enhancing seed sustainability in Bandung District
  110. Evaluation of Abrams curve in agricultural sector using the NARDL approach
  111. Challenges and opportunities for young farmers in the implementation of the Rural Development Program 2014–2020 of the Republic of Croatia
  112. Yield stability of ten common bean (Phaseolus vulgaris L.) genotypes at different sowing dates in Lubumbashi, South-East of DR Congo
  113. Effects of encapsulation and combining probiotics with different nitrate forms on methane emission and in vitro rumen fermentation characteristics
  114. Phytochemical analysis of Bienertia sinuspersici extract and its antioxidant and antimicrobial activities
  115. Evaluation of relative drought tolerance of grapevines by leaf fluorescence parameters
  116. Yield assessment of new streak-resistant topcross maize hybrids in Benin
  117. Improvement of cocoa powder properties through ultrasonic- and microwave-assisted alkalization
  118. Potential of ecoenzymes made from nutmeg (Myristica fragrans) leaf and pulp waste as bioinsecticides for Periplaneta americana
  119. Analysis of farm performance to realize the sustainability of organic cabbage vegetable farming in Getasan Semarang, Indonesia
  120. Revealing the influences of organic amendment-derived dissolved organic matter on growth and nutrient accumulation in lettuce seedlings (Lactuca sativa L.)
  121. Identification of viruses infecting sweetpotato (Ipomoea batatas Lam.) in Benin
  122. Assessing the soil physical and chemical properties of long-term pomelo orchard based on tree growth
  123. Investigating access and use of digital tools for agriculture among rural farmers: A case study of Nkomazi Municipality, South Africa
  124. Does sex influence the impact of dietary vitD3 and UVB light on performance parameters and welfare indicators of broilers?
  125. Design of intelligent sprayer control for an autonomous farming drone using a multiclass support vector machine
  126. Deciphering salt-responsive NB-ARC genes in rice transcriptomic data: A bioinformatics approach with gene expression validation
  127. Review Articles
  128. Impact of nematode infestation in livestock production and the role of natural feed additives – A review
  129. Role of dietary fats in reproductive, health, and nutritional benefits in farm animals: A review
  130. Climate change and adaptive strategies on viticulture (Vitis spp.)
  131. The false tiger of almond, Monosteira unicostata (Hemiptera: Tingidae): Biology, ecology, and control methods
  132. A systematic review on potential analogy of phytobiomass and soil carbon evaluation methods: Ethiopia insights
  133. A review of storage temperature and relative humidity effects on shelf life and quality of mango (Mangifera indica L.) fruit and implications for nutrition insecurity in Ethiopia
  134. Green extraction of nutmeg (Myristica fragrans) phytochemicals: Prospective strategies and roadblocks
  135. Potential influence of nitrogen fertilizer rates on yield and yield components of carrot (Dacus carota L.) in Ethiopia: Systematic review
  136. Corn silk: A promising source of antimicrobial compounds for health and wellness
  137. State and contours of research on roselle (Hibiscus sabdariffa L.) in Africa
  138. The potential of phosphorus-solubilizing purple nonsulfur bacteria in agriculture: Present and future perspectives
  139. Minor millets: Processing techniques and their nutritional and health benefits
  140. Meta-analysis of reproductive performance of improved dairy cattle under Ethiopian environmental conditions
  141. Review on enhancing the efficiency of fertilizer utilization: Strategies for optimal nutrient management
  142. The nutritional, phytochemical composition, and utilisation of different parts of maize: A comparative analysis
  143. Motivations for farmers’ participation in agri-environmental scheme in the EU, literature review
  144. Evolution of climate-smart agriculture research: A science mapping exploration and network analysis
  145. Short Communications
  146. Music enrichment improves the behavior and leukocyte profile of dairy cattle
  147. Effect of pruning height and organic fertilization on the morphological and productive characteristics of Moringa oleifera Lam. in the Peruvian dry tropics
  148. Corrigendum
  149. Corrigendum to “Bioinformatics investigation of the effect of volatile and non-volatile compounds of rhizobacteria in inhibiting late embryogenesis abundant protein that induces drought tolerance”
  150. Corrigendum to “Composition and quality of winter annual agrestal and ruderal herbages of two different land-use types”
  151. Special issue: Smart Agriculture System for Sustainable Development: Methods and Practices
  152. Construction of a sustainable model to predict the moisture content of porang powder (Amorphophallus oncophyllus) based on pointed-scan visible near-infrared spectroscopy
  153. FruitVision: A deep learning based automatic fruit grading system
  154. Energy harvesting and ANFIS modeling of a PVDF/GO-ZNO piezoelectric nanogenerator on a UAV
  155. Effects of stress hormones on digestibility and performance in cattle: A review
  156. Special Issue of The 4th International Conference on Food Science and Engineering (ICFSE) 2022 - Part II
  157. Assessment of omega-3 and omega-6 fatty acid profiles and ratio of omega-6/omega-3 of white eggs produced by laying hens fed diets enriched with omega-3 rich vegetable oil
  158. Special Issue on FCEM - International Web Conference on Food Choice & Eating Motivation - Part II
  159. Special Issue on FCEM – International Web Conference on Food Choice & Eating Motivation: Message from the editor
  160. Fruit and vegetable consumption: Study involving Portuguese and French consumers
  161. Knowledge about consumption of milk: Study involving consumers from two European Countries – France and Portugal
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