Soil microbiomes from the groundnut basin of Senegal contain plant growth-promoting bacteria with potential for crop improvement in arid soils

The principal methods to maintain soil fertility in Sahel soils are largely allowing fields to go fallow and manure addition. These methods are not currently sufficient to improve soil fertility. To promote biological amendments, we aimed to understand the plant-growth promoting traits of various soil microbial isolates. The soils collected in different areas in Senegal exhibited a similar eDNA profile of bacteria; the dominant microbes were Firmicutes, followed by Proteobacteria and Actinobacteria. Of 17 isolates identified and tested, the vast majority solubilized rock phosphate and a large number grew on culture medium containing 6% salt, but very few degraded starches or hydrolysed carboxymethyl cellulose or produced siderophores. Upon single inoculation, Peribacillus asahii RC16 and Dietzia cinnamea 55 significantly increased pearl millet growth and yield parameters. For cowpea, plant shoot length was significantly increased by Pseudarthrobacter phenanthrenivorans MKAG7 co-inoculated with Bradyrhizobium elkanii 20TpCR5, and nearly all rhizobacteria tested significantly improved cowpea dry weight and pod weight. Additionally, the double inoculation of Dietzia cinnamea 55 and MKAG7 significantly increased shoot length, dry weight, and seed head weight of pearl millet. These isolates are promising inoculants because they are ecologically-friendly, cost-effective, sustainable, and have fewer negative effects on the soil and its inhabitants.

Breeding and biotechnology approaches to enhance the nutritional quality of rapeseed byproducts for sustainable alternative protein sources- a critical review

Global protein consumption is increasing exponentially, which requires efficient identification of potential, healthy, and simple protein sources to fulfil the demands. The existing sources of animal proteins are high in fat and low in fiber composition, which might cause serious health risks when consumed regularly. Moreover, protein production from animal sources can negatively affect the environment, as it often requires more energy and natural resources and contributes to greenhouse gas emissions. Thus, finding alternative plant-based protein sources becomes indispensable. Rapeseed is an important oilseed crop and the world's third leading oil source. Rapeseed byproducts, such as seed cakes or meals, are considered the best alternative protein source after soybean owing to their promising protein profile (30%-60% crude protein) to supplement dietary requirements. After oil extraction, these rapeseed byproducts can be utilized as food for human consumption and animal feed. However, anti-nutritional factors (ANFs) like glucosinolates, phytic acid, tannins, and sinapines make them unsuitable for direct consumption. Techniques like microbial fermentation, advanced breeding, and genome editing can improve protein quality, reduce ANFs in rapeseed byproducts, and facilitate their usage in the food and feed industry. This review summarizes these approaches and offers the best bio-nutrition breakthroughs to develop nutrient-rich rapeseed byproducts as plant-based protein sources.

Unraveling the potential of bacterial phytases for sustainable management of phosphorous

Phosphorous actively participates in numerous metabolic and regulatory activities of almost all living organisms including animals and humans. Therefore, it is considered as an essential macronutrient required supporting their proper growth. On contrary, phytic acid (PA), an antinutritional substance, is widely known for its strong affinity to chelate essential mineral ions including PO4 3- , Ca2+ , Fe2+ , Mg2+ , and Zn2+ . Being one the major reservoir of PO4 3- ions, PA has great potential to bind PO4 3- ions in diverse range of foods. Once combined with P, PA transforms into an undigested and insoluble complex namely phytate. Produced phytate leads to a notable reduction in the bioavailability of P due to negligible activity of phytases in monogastric animals and humans. This highlights the importance and consequent need of enhancement of phytase level in these life forms. Interestingly, phytases, catalyzing the breakdown of phytate complex and recycling the phosphate into ecosystem to its available form, have naturally been reported in a variety of plants and microorganisms over past few decades. In pursuit of a reliable solution, the focus of this review is to explore the keynote potential of bacterial phytases for sustainable management of phosphorous via efficient utilization of soil phytate. The core of the review covers detailed discussion on bacterial phytases along with their widely reported applications viz. biofertilizers, phosphorus acquisition, and plant growth promotion. Moreover, meticulous description on fermentation-based strategies and future trends on bacterial phytases have also been included.

Abundance and phylogenetic distribution of eight key enzymes of the phosphorus biogeochemical cycle in grassland soils

Grassland biomes provide valuable ecosystem services, including nutrient cycling. Organic phosphorus (Po) represents more than half of the total P in soils. Soil microorganisms release organic P through enzymatic processes, with alkaline phosphatases, acid phosphatases and phytases being the key P enzymes involved in the cycling of organic P. This study analysed 74 soil metagenomes from 17 different grassland biomes worldwide to evaluate the distribution and abundance of eight key P enzymes (PhoD, PhoX, PhoA, Nsap-A, Nsap-B, Nsap-C, BPP and CPhy) and their relationship with environmental factors. Our analyses showed that alkaline phosphatase phoD was the dataset's most abundant P-enzyme encoding genes, with a wide phylogenetic distribution. Followed by the acid phosphatases Nsap-A and Nsap-C showed similar abundance but a different distribution in their respective phylogenetic trees. Multivariate analyses revealed that pH, Tmax , SOC and soil moisture were associated with the abundance and diversity of all genes studied. PhoD and phoX genes strongly correlated with SOC and clay, and the phoX gene was more common in soils with low to medium SOC and neutral pH. In particular, P-enzyme genes tended to respond in a positively correlated manner among them, suggesting a complex relationship of abundance and diversity among them.

Effects of long-term irrigation on soil phosphorus fractions and microbial communities in Populus euphratica plantations

Irrigation has been demonstrated to be effective in managing Populus euphratica plantations, but its impacts on phosphorus (P) availability and the soil microbiome have not been fully elucidated. In this study, we compared soil properties, P fractions, phosphatase activities, and microbial communities in the surface soil (0-20 cm) of P. euphratica plantations under both drought and irrigation conditions. We found that total P, labile P and moderately labile P all increased significantly under irrigation by 12.3%, 70.1%, and 3.0%, respectively. The increased levels of labile P were primarily driven by higher levels of NaHCO3-Pi, which increased from 1.9 to 12.3 mg·kg-1. Furthermore, irrigation markedly altered labile P composition and the relative levels of resin P, NaHCO3-Pi, and NaHCO3-Po were all impacted. Improved soil moisture increased soil phosphatase activity, suggesting that soil organic P (Po) mineralization was positively affected by irrigation. Moreover, we observed that bacterial diversity, fungal diversity, and alkaline phosphatase gene communities, rather than total microbial biomass carbon or total phospholipid fatty acids, were most explained in the dynamics of soil P fractions. Furthermore, we found positive correlations among inorganic P (Pi) and Bradyrhizobiaceae, Nocardiaceae, and Sphingomonadaceae, whereas negative correlations were found between Burkholderiaceae and Pi, highlighting the diverse functional bacteria involved in P cycling. Our study demonstrates that irrigation can increase soil P availability and supply capacity, with shifts in P composition closely linked to changes in soil microbial characteristics. Water management strategies that target the restoration of soil microbial communities may therefore improve soil quality and enhance soil P cycling.

Seed phytic acid concentration affects rice seedling vigor irrespective of soil phosphorus bioavailability

Rice with a black-colored pericarp (hereafter, black rice) is well-known as an antioxidant-rich food, but a high grain phytic acid (PA) concentration affects its nutritional quality. However, phytic acid helps improve seedling vigor, which is crucial for enhancing subsequent plant growth. This study investigated the effect of seed phytic acid concentration in black rice on seedling vigor compared to the effects on white rice. In the first experiment, three phytic acid concentrations in the seeds of black rice, low (LPA, 15.5 mg g^-1 per seed), medium (MPA, 24.7 mg g^-1 per seed), and high (HPA, 35.4 mg g^-1 per seed) were tested for seedling vigor in phosphorus-deficient soils. The HPA seedlings showed substantially increased seedling vigor and shoot P uptake due to early root development and enhanced physiological processes. LPA grown seedlings showed increased ethylene production in response to P stress, which is the main physiological mechanism modulating seedling growth under P stress conditions. In the second experiment, the three phytic acid concentrations in black and white rice seeds were tested under low and high soil P conditions. Again, LPA seedlings showed significantly reduced seedling vigor in both rice varieties in P-deficient soils. Interestingly, seed phytic acid and external P application had an additive effect on seedling vigor, suggesting that the combined effect further improved seedling growth. Our results reveal that black rice seeds with a HPA concentration can be used as a seed source for planting in P-deficient ecosystems for rice plants as they can increase seedling vigor and subsequent growth, thus reducing dependence on finite P resources.

Wide-genome selection of lactic acid bacteria harboring genes that promote the elimination of antinutritional factors

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 Bacillus subtilis 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 Lactobacillus and Pediococcus 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 B. subtilis and Pediococcus 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 B. subtilis 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.

Insight into phytase-producing microorganisms for phytate solubilization and soil sustainability

The increasing demand for food has increased dependence on chemical fertilizers that promote rapid growth and yield as well as produce toxicity and negatively affect nutritional value. Therefore, researchers are focusing on alternatives that are safe for consumption, non-toxic, cost-effective production process, and high yielding, and that require readily available substrates for mass production. The potential industrial applications of microbial enzymes have grown significantly and are still rising in the 21st century to fulfill the needs of a population that is expanding quickly and to deal with the depletion of natural resources. Due to the high demand for such enzymes, phytases have undergone extensive research to lower the amount of phytate in human food and animal feed. They constitute efficient enzymatic groups that can solubilize phytate and thus provide plants with an enriched environment. Phytases can be extracted from a variety of sources such as plants, animals, and microorganisms. Compared to plant and animal-based phytases, microbial phytases have been identified as competent, stable, and promising bioinoculants. Many reports suggest that microbial phytase can undergo mass production procedures with the use of readily available substrates. Phytases neither involve the use of any toxic chemicals during the extraction nor release any such chemicals; thus, they qualify as bioinoculants and support soil sustainability. In addition, phytase genes are now inserted into new plants/crops to enhance transgenic plants reducing the need for supplemental inorganic phosphates and phosphate accumulation in the environment. The current review covers the significance of phytase in the agriculture system, emphasizing its source, action mechanism, and vast applications.

Enhancing Phytate Availability in Soils and Phytate-P Acquisition by Plants: A Review

Phytate (myo-inositol hexakisphosphate salts) can constitute a large fraction of the organic P in soils. As a more recalcitrant form of soil organic P, up to 51 million metric tons of phytate accumulate in soils annually, corresponding to ∼65% of the P fertilizer application. However, the availability of phytate is limited due to its strong binding to soils via its highly-phosphorylated inositol structure, with sorption capacity being ∼4 times that of orthophosphate in soils. Phosphorus (P) is one of the most limiting macronutrients for agricultural productivity. Given that phosphate rock is a finite resource, coupled with the increasing difficulty in its extraction and geopolitical fragility in supply, it is anticipated that both economic and environmental costs of P fertilizer will greatly increase. Therefore, optimizing the use of soil phytate-P can potentially enhance the economic and environmental sustainability of agriculture production. To increase phytate-P availability in the rhizosphere, plants and microbes have developed strategies to improve phytate solubility and mineralization by secreting mobilizing agents including organic acids and hydrolyzing enzymes including various phytases. Though we have some understanding of phytate availability and phytase activity in soils, the limiting steps for phytate-P acquisition by plants proposed two decades ago remain elusive. Besides, the relative contribution of plant- and microbe-derived phytases, including those from mycorrhizas, in improving phytate-P utilization is poorly understood. Hence, it is important to understand the processes that influence phytate-P acquisition by plants, thereby developing effective molecular biotechnologies to enhance the dynamics of phytate in soil. However, from a practical view, phytate-P acquisition by plants competes with soil P fixation, so the ability of plants to access stable phytate must be evaluated from both a plant and soil perspective. Here, we summarize information on phytate availability in soils and phytate-P acquisition by plants. In addition, agronomic approaches and biotechnological strategies to improve soil phytate-P utilization by plants are discussed, and questions that need further investigation are raised. The information helps to better improve phytate-P utilization by plants, thereby reducing P resource inputs and pollution risks to the wider environment.

Green Synthesis of Gold Nanoparticles: An Eco-Friendly Approach

By virtue of their unique physicochemical properties, gold nanoparticles (AuNPs) have gained significant interest in a broad range of biomedical applications such as sensors, diagnosis, and therapy. AuNPs are generally synthesized via different conventional physical and chemical methods, which often use harmful chemicals that induce health hazards and pollute the environment. To overcome these issues, green synthesis techniques have evolved as alternative and eco-friendly approaches to the synthesis of environmentally safe and less-expensive nanoparticles using naturally available metabolites from plants and microorganisms such as bacteria, fungi, and algae. This review provides an overview of the advances in the synthesis of AuNPs using different biological resources with examples, and their profound applications in biomedicine. A special focus on the biosynthesis of AuNPs using different medicinal plants and their multifunctional applications in antibacterial, anti-inflammatory, and immune responses are featured. Additionally, the applications of AuNPs in cancer theranostics, including contrast imaging, drug delivery, hyperthermia, and cancer therapeutics, are comprehensively discussed. Moreover, this review will shed light on the importance of the green synthesis approach, and discuss the advantages, challenges, and prospects in this field.

A novel phytase from Citrobactergillenii: characterization and expression in Pichia pastoris (Komagataella pastoris)

The phyCg gene encoding a new phytase from Citrobacter gillenii was optimized, synthesized, cloned and expressed in Pichia pastoris. Analysis of the amino acid sequence of the enzyme showed that it belongs to the histidine acid phosphatase family. The amino acid sequence of the PhyCg phytase has the highest homology (73.49%) with a phytase sequence from Citrobacter braakii. The main characteristics for the purified recombinant phytase were established. The optimum pH and temperature were 4.5 and 50°C, respectively. The specific activity of the enzyme was 1577 U/mg. The Michaelis constant (Km) and the maximum reaction rate (Vmax) for sodium phytate were 0.185 mM and 2185 U/mg, respectively. The enzyme showed the pH and trypsin stability and had a high activity over a wide pH range.

The grazing activity of Acrobeloides sp. drives phytate mineralisation within its trophic relationship with bacteria

The microbial loop has been suggested as an alternative route for better utilization of phytate, a poorly available P source to plants. We hypothesized that bacterial grazer activity might dramatically enhance bacterial migration and proliferation, increasing the probability of phytate hydrolysis by bacterial phytases and, thus, phytate mineralization and release of free phosphate. We tested this hypothesis in a two-compartment system with a solid medium containing phytate or free phosphate as the source of P. Two bacterial species, B. subtilis 168 or Bradyrhizobium sp., with or without bacterial grazing nematodes belonging to Acrobeloides sp. previously fed on each of the bacterial species, were inoculated at a single point in the medium. Whatever the P source, nematode migration within both zones allowed the proliferation of bacteria. However, B. subtilis 168 was more efficient in using phytate than Bradyrhizobium sp. since the highest bacterial cell density and free phosphate concentrations were reached by Acrobeloides sp. fed on B. subtilis 168. The grazer activity seemed to be crucial to enhance phytate mineralization, despite Acrobeloides sp. showing a higher preference to feed on Bradyrhizobium sp. This study provides new insights into the effects of bacterial grazer activity on phytate mineralization.

Contrasting Expression of Rhizobial Phytase in Nodules of Two Soybean Cultivars Grown Under Low Phosphorus Availability

Phosphorus deficiency can be a major limitation to legume growth when plant nitrogen nutrition depends on symbiotic nitrogen fixation. One possible approach to overcome this constraint is the selection of plant and rhizobial genotypes capable of metabolizing complex forms of phosphorus in the nodules. The aim of this research was to study the rhizobial phytase transcript abundance in nodules of two soybean cultivars (Glycine max (L.) Merr.) grown under two different phosphorus conditions in hydroaeroponic conditions. An in situ RT-PCR of a rhizobial phytase was performed in microtome sections of soybean nodules of two cultivars growing under phosphorus sufficiency vs. phosphorus deficiency. The results showed that the plant cultivar may influence the level of transcript abundance of the bacterial phytase and in consequence affect the phosphorus use efficiency of nitrogen-dependent Bradyrhizobium spp.-soybean symbioses. Thus, the selection of a good combination of plant and rhizobial genotypes should be a priority when breeding for phosphorus deficiency is performed.

Reevaluation of Phytase Action Mechanism in Animal Nutrition

The release of phosphorus from phytates occurs via sequential cleavage of phosphate groups. It was believed that, regardless of the properties of phytases, the rate of phytate dephosphorylation is limited by the first cleavage of any phosphate group. The position of the first cleaved-off phosphate group depending on the specificity of phytase. The inhibition of dephosphorylation initiation is not associated with the action mechanism of the enzyme and can be rather due to the insufficient phytase activity or low availability of phytates. The analysis of the transformations in the inositol hexakisphosphate (IP₆)→inositol (I) reaction chain shows that IP₆ dephosphorylation as a whole limits the phosphate group removal from I(1,2,5,6)P₄ (third reaction from the beginning of hydrolysis of phosphate bonds in PA). The lower availability of nutrients in the presence of phytates is not due to action of phytates, but is caused by PA anions (IP_6-3), which bind positively charged metal ions, amino acids, and proteins. The availability of nutrients increases as a result of the decrease in their binding caused by the decrease in the concentration of IP_(6-3) anions under the action of phytases. Phytases added to feeds play a lesser role in the digestion of phytates compared to natural enzymes and complement their action. The concept of extra-phosphoric effect has no scientific justification, since phytases exhibit only the phosphohydrolase activity and are not able to catalyze other reactions.

Diverse role of phytic acid in plants and approaches to develop low-phytate grains to enhance bioavailability of micronutrients

Natural or synthetic compounds that interfere with the bioavailability of nutrients are called antinutrients. Phytic acid (PA) is one of the major antinutrients present in the grains and acts as a chelator of micronutrients. The presence of six reactive phosphate groups in PA hinders the absorption of micronutrients in the gut of non-ruminants. Consumption of PA-rich diet leads to deficiency of minerals such as iron and zinc among human population. On the contrary, PA is a natural antioxidant, and PA-derived molecules function in various signal transduction pathways. Therefore, optimal concentration of PA needs to be maintained in plants to avoid adverse pleiotropic effects, as well as to ensure micronutrient bioavailability in the diets. Given this, the chapter enumerates the structure, biosynthesis, and accumulation of PA in food grains followed by their roles in growth, development, and stress responses. Further, the chapter elaborates on the antinutritional properties of PA and explains the conventional breeding and transgene-based approaches deployed to develop low-PA varieties. Studies have shown that conventional breeding methods could develop low-PA lines; however, the pleiotropic effects of these methods viz. reduced yield, embryo abnormalities, and poor seed quality hinder the use of breeding strategies. Overexpression of phytase in the endosperm and RNAi-mediated silencing of genes involved in myo-inositol biosynthesis overcome these constraints. Next-generation genome editing approaches, including CRISPR-Cas9 enable the manipulation of more than one gene involved in PA biosynthesis pathway through multiplex editing, and scope exists to deploy such tools in developing varieties with optimal PA levels.

Soil quality parameters vis-a-vis growth and yield attributes of sugarcane as influenced by integration of microbial consortium with NPK fertilizers

Intensive agriculture involving high crop intensity, unavailability of organics, and higher use of straight fertilizers causes imbalanced use and deficiencies of several other macro and micronutrients. Nutrients supply through the integration of microbial consortium containing Gluconacetobater diazotrophicus, Trichoderma harzianum, and Pseudomonas fluorescens can reduce the requirements on the one hand and can also increase the response of chemical fertilizers. Thus we had planned the present experiment with the objectives (i) to determine the effect of integrated application of microbial consortium (MC) and NPK fertilizer on soil quality parameters and crop growth and yield attributes and (ii) to assess the effect of integration on agronomic efficiency of N, P and K and find out the possibilities for reduction in applied doses of NPK, if any. Five treatments viz., T₁; N₀P₀K₀; T₂: N₇₅P₁₃K₂₅; T₃: N₁₅₀P₂₆K₅₀; T₄: N₇₅P₁₃K₂₅ + microbial consortium and T₅: N₁₅₀P₂₆K₅₀ + microbial consortium containing new strains of Trichoderma harzianum, Gluconcetobacter diazotrophicus, and Pseudomonas fluorescens (CFU 10^9–10 per ml liquid culture) were evaluated under four replications in a randomized block design (RBD). Experimental results indicated that integrating microbial consortium and NPK fertilizers' application proved effective in improving soil organic carbon, soil microbial population, microbial biomass carbon, microbial biomass nitrogen, and soil respiration. Integrated use of microbial consortium with NPK also improved the cation exchange capacity of soil and roots. However, the growth and yield attributes, nutrients uptake, sugarcane, and sugar yields also revealed a positive effect of microbial consortium's integrated application with NPK. The integration of MC and NPK also improved the agronomic efficiency of applied nutrients (NPK). Reduction of 50% NPK with these microbial consortia (Trichoderma harzianum, Gluconcetobacter diazotrophicus, and Pseudomonas fluorescens) was found better than the application of full NPK through chemical fertilizers. Thus application of N₁₅₀P₂₆K₅₀ with microbial consortium can sustain soil fertility besides improving sugarcane and sugar yields in subtropical Indian conditions.

Spatial variation of the soil bacterial community in major apple producing regions of China

AIMS

In China, apple production areas are largely from the coastal to inland areas and across varied climate zones. However, the relationship among soil micro-organisms, environmental factors and fruit quality has not been clearly confirmed in orchards. Here we attempted to identify the variation of soil bacteria in the main apple producing regions and reveal the relationship among climatic factor, soil properties, soil bacterial community and fruit quality.

METHODS AND RESULTS

Sixty soil samples were collected from six main apple producing areas in China. We examined the soil bacteria using bacterial 16S rRNA gene amplicon profiling. The results show that the soil bacterial diversity of apple orchards varied from the Bohai Bay Region to the Loess Plateau Region. Proteobacteria, Acidobacteria and Actinobacteria were the predominant taxa at the phylum level for all six areas. In the Bohai Bay and the Loess Plateau region, which are the two largest apple producing areas, Proteobacteria and Actinobacteria had the highest relative abundance, respectively. Furthermore, soil bacterial diversity showed positive correlation with the mean annual temperature (MAT), soil organic matter (SOM) and pH. Excluding a direct effect on the apple fruit quality, MAT exerted an indirect influence through soil SOM and pH to alter the relative abundance of dominant taxa and shift the bacterial diversity, which affects the apple fruit titratable acids and soluble solids.

CONCLUSIONS

Geographic variables underlie apple orchard soil bacterial communities vary according to spatial scale. Environmental factors exert an indirect effect on apple fruit quality via shaping soil bacterial community.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study provides a list of bacteria associated with environmental factors and the ecological attributes of their interactions in apple orchards, which will improve our ability to promote soil bacterial functional capabilities in order to reduce the fertilizer input and enhance the fruit quality.

Biocontrol of tobacco black shank disease (Phytophthora nicotianae) by Bacillus velezensis Ba168

Tobacco black shank (TBS) caused by Phytophthora nicotianae is destructive to almost all tobacco cultivars and is widespread in many tobacco-growing countries. Through lab study and field test, we isolated plant growth-promoting rhizobacteria (PGPR) strain Ba168 which is a promising biocontrol strain of TBS. Ba168 was isolated from 168 soil samples and identified as Bacillus velezensis by its genetic and phenotypic characteristics. A susceptibility test indicated that the P. nicotianae antagonistic materials of Ba168 in extracellular metabolites were composed of effective and stable proteins/peptides. P. nicotianae's growth was suppressed by the ammonium sulfate precipitation of Ba168 culture filtrates (ASPBa) at a minimum inhibitory concentration of 5 μg/mL. Extracellular conductivity, pH, and the wet/dry weights of P. nicotianae's mycelia, along with scanning electron microscope analysis, suggested that Ba168-derived proteins/peptides could effectively inhibit P. nicotianae by causing irreversible damage to its cell walls and membranes. Protein identification of ASPBa supported these results and identified many key proteins responsible for various biocontrol-related pathways. Field assays of TBS control efficacy of many PGPRs and agrochemicals showed that all PGPR preparations reduced the disease index of tobacco, but Ba168 was the most effective. These results demonstrated the importance of Bacillus-derived proteins/peptides in the inhibition of P. nicotianae through irreversible damage to its cell wall and membrane; and the effectiveness of PGPR strain B. velezensis Ba168 for biocontrol of the soil-borne disease caused by P. nicotianae.

Development and validation of breeder-friendly gene-based markers for lpa1-1 and lpa2-1 genes conferring low phytic acid in maize kernel

Based on C (wild) to T (mutant) transition at amino acid position 1432 bp of lpa1-1 gene, two dominant markers each specific to wild type (LPA1) and mutant (lpa1-1) allele were developed and validated across seven F₂ populations. Joint segregation of these markers behaved in co-dominant fashion, clearly distinguishing heterozygote from two other homozygote genotypes. Full length sequence alignment between wild type (LPA2) and mutant (lpa2-1) allele revealed one transition mutation (A to G) and a co-dominant CAPS marker was developed which differentiated all three types of segregants across seven F₂ populations. Across populations, segregants with lpa1-1/lpa1-1 (1.77 mg/g) and lpa2-1/lpa2-1 (1.85 mg/g) possessed significantly lower phytic acid compared to LPA1/LPA1 (2.58 mg/g) and LPA2/LPA2 (2.53 mg/g). Inorganic phosphorus was however higher in recessive homozygotes (lpa1-1/lpa1-1: 0.77 mg/g, lpa2-1/lpa2-1: 0.53 mg/g) than the dominant homozygotes (LPA1/LPA1: 0.33 mg/g, LPA2/LPA2: 0.19 mg/g). Overall, homozygous segregants of lpa1-1 and lpa2-1 showed 31% and 27% reduction of phytic acid, respectively. Analysis of phytate and inorganic phosphorous in the maize kernel in these segregating populations confirmed co-segregation of trait and markers specific to lpa1-1 and lpa2-1. This is the first report of the development of breeder-friendly gene-based markers for lpa1-1 and lpa2-1; and it holds great significance for maize biofortification.

Molecular Breeding for Nutritionally Enriched Maize: Status and Prospects

Maize is a major source of food security and economic development in sub-Saharan Africa (SSA), Latin America, and the Caribbean, and is among the top three cereal crops in Asia. Yet, maize is deficient in certain essential amino acids, vitamins, and minerals. Biofortified maize cultivars enriched with essential minerals and vitamins could be particularly impactful in rural areas with limited access to diversified diet, dietary supplements, and fortified foods. Significant progress has been made in developing, testing, and deploying maize cultivars biofortified with quality protein maize (QPM), provitamin A, and kernel zinc. In this review, we outline the status and prospects of developing nutritionally enriched maize by successfully harnessing conventional and molecular marker-assisted breeding, highlighting the need for intensification of efforts to create greater impacts on malnutrition in maize-consuming populations, especially in the low- and middle-income countries. Molecular marker-assisted selection methods are particularly useful for improving nutritional traits since conventional breeding methods are relatively constrained by the cost and throughput of nutritional trait phenotyping.

Lactic Fermentation as a Strategy to Improve the Nutritional and Functional Values of Pseudocereals

One of the greatest challenges is to reduce malnutrition worldwide while promoting sustainable agricultural and food systems. This is a daunting task due to the constant growth of the population and the increasing demands by consumers for functional foods with higher nutritional values. Cereal grains are the most important dietary energy source globally; wheat, rice, and maize currently provide about half of the dietary energy source of humankind. In addition, the increase of celiac patients worldwide has motivated the development of gluten-free foods using alternative flour types to wheat such as rice, corn, cassava, soybean, and pseudocereals (amaranth, quinoa, and buckwheat). Amaranth and quinoa have been cultivated since ancient times and were two of the major crops of the Pre-Colombian cultures in Latin- America. In recent years and due to their well-known high nutritional value and potential health benefits, these pseudocereals have received much attention as ideal candidates for gluten-free products. The importance of exploiting these grains for the elaboration of healthy and nutritious foods has forced food producers to develop novel adequate strategies for their processing. Fermentation is one of the most antique and economical methods of producing and preserving foods and can be easily employed for cereal processing. The nutritional and functional quality of pseudocereals can be improved by fermentation using Lactic Acid Bacteria (LAB). This review provides an overview on pseudocereal fermentation by LAB emphasizing the capacity of these bacteria to decrease antinutritional factors such as phytic acid, increase the functional value of phytochemicals such as phenolic compounds, and produce nutritional ingredients such as B-group vitamins. The numerous beneficial effects of lactic fermentation of pseudocereals can be exploited to design novel and healthier foods or grain ingredients destined to general population and especially to patients with coeliac disease.

Phosphorus forms affect the hyphosphere bacterial community involved in soil organic phosphorus turnover

Interactions between bacteria and arbuscular mycorrhizal (AM) fungi play a significant role in mediating organic phosphorus (P) transformations and turnover in soil. The bacterial community in soil is largely responsible for mobilization of the soil organic P pool, and the released P is taken up by extraradical AM hyphae, which mediate its use for plant growth. However, the functional microbiome involved in organic P mineralization in the hyphosphere remains poorly understood. The aim of this study was to determine how AM hyphae-associated bacterial communities related to P turnover in the hyphosphere of leek (Allium porrum) respond to different forms of soil P. Using a compartmented microcosm, leek was grown with the AM fungus Funneliformis mosseae, and the extraradical mycelium of F. mosseae was allowed to grow into a separate hyphal compartment containing either no added P, or P as KH₂PO₄ or phytin. High-throughput sequencing showed that the alkaline phosphatase (ALP)-harboring bacterial community associated with the AM hyphae was dominated by Sinorhizobium, Bradyrhizobium, Pseudomonas, and Ralstonia and was significantly changed in response to different P treatments, with Pseudomonas showing higher relative abundance in organic P treatments than in control and inorganic P treatments. Pseudomonas was also the major genus harboring the β-propeller phytase (BPP) gene in the hyphosphere, but the BPP-harboring community structure was not affected by the presence of different P forms. These results demonstrate the profound differences in ALP- and BPP-harboring bacterial communities in the hyphosphere at bacterial genus level, providing new insights to link bacteria and biogeochemical P cycling driven in association with mycorrhizal hyphae.

Exploring Bacterial Communities in Aquaponic Systems

Aquaponics is a production system based on the dynamic equilibrium between fish, plants, and microorganisms. In order to better understand the role of microorganisms in this tripartite relationship, we studied the bacterial communities hosted in eight aquaponic and aquaculture systems. The bacterial communities were analyzed by 16S rRNA gene deep sequencing. At the phylum level, the bacterial communities from all systems were relatively similar with a predominance of Proteobacteria and Bacteroidetes. At the genus level, however, the communities present in the sampled systems were more heterogeneous. The biofilter samples harbored more diverse communities than the corresponding sump samples. The core microbiomes from the coupled and decoupled systems shared more common operational taxonomic units than with the aquaculture systems. Eventually, some of the taxa identified in the systems could have beneficial functions for plant growth and health, but a deeper analysis would be required to identify the precise functions involved in aquaponics.

Current and Future Applications of Phytases in Poultry Industry: A Critical Review

Phytases are enzymes that initiate the removal of phosphate from phytate. This enzyme has been widely utilized in animal feeding especially in the poultry industry to enhance phosphorus intake and minimize environmental pollution. Phytases are widely distributed in microbial, plants and animals. Supplementations of phytase into the diets of poultry have great impact to the improvement of poultry immune systems and increase bird weight. In addition to that, phytase are able to improve both quantity and quality of eggs, egg mass and egg shell quality. This review covers the classifications and distribution of phytases in different biofactoris. In addition, it shed more light on the recent trends of application and beneficial impact in poultry farming.

Apple rootstocks of different nitrogen tolerance affect the rhizosphere bacterial community composition

AIMS

To select apple rootstocks that are tolerant to low nitrogen and reveal the relationship between the rhizosphere bacterial communities and the low nitrogen tolerance of the apple rootstock.

METHODS AND RESULTS

In total, 235 lines of hybrids of Malus robusta Rehd. × M.9 with low nitrogen stress were cultivated in pots in a greenhouse equipped with a drip irrigation system, and growth characteristics, photosynthesis traits and mineral elements were monitored. The bacterial community structure of the rhizosphere from different rootstocks was determined via Illumina MiSeq sequencing. This study selected three low nitrogen-tolerant (NT) lines that had higher nitrogen concentration, and higher photosynthesis rate than the three low nitrogen-sensitive (NS) lines. The bacterial community structure significantly differed (P ≤ 0·001) among the rootstocks. The bacterial phyla Proteobacteria and Actinobacteria were the dominant groups in the rhizosphere and presented higher abundance in the NT rhizosphere. The N concentration in the apple rootstocks exhibited highly positive Pearson correlations with the bacterial genera Sphingomonas, Pseudoxanthomonas, Bacillus and Acinetobacter, and negative correlations with the bacterial genera Pseudarthrobacter and Bradyrhizobium.

CONCLUSIONS

This study showed that investigated rootstocks achieved increased nitrogen concentration by enhancing their photosynthetic production capacity and shaping their rhizobacteria community structure.

SIGNIFICANCE AND IMPACT OF THE STUDY

The findings provide a basis for studying the mechanisms of resistance to low nitrogen stress in apple rootstocks. Based on these beneficial bacteria, microbial inoculants can be developed for use in sustainable agricultural and horticultural production.

A novel purple acid phytase from an earthworm cast bacterium

BACKGROUND

Phytases are a diverse group of enzymes initiating the dephosphorylation of phytate. Phytate is considered as an anti-nutritional compound because of its capability to chelate nutrients such as Fe²⁺ , Zn²⁺ , Mg²⁺ , and Ca²⁺ . In this study, several bacterial isolates obtained from earthworm casts were evaluated for their phytate degrading capability. Enzymatic properties and the sequence of the corresponding phytase-encoding gene of the selected isolate were determined.

RESULTS

The phytase exhibited its highest activity at pH 4.0 and was stable from pH 3 up to pH 9. The temperature optimum was determined to be 65 °C. The strongest inhibitors of enzymatic activity were identified as vanadate, Cu²⁺ , and Zn²⁺ . High-performance ion chromatography analysis of enzymatic phytate dephosphorylation revealed that the first dephosphorylation product was d/l-myo-inositol(1,2,3,4,5)pentakisphosphate.

CONCLUSION

Owing to its enzymatic properties, such as tolerance to tartrate and the presence of the consensus motifs PDTVY, GNHE, DLG, VLFH, and GHDH, this phytase could be classified as a purple acid phytase. To the best of our knowledge, this is the first report describing a bacterial purple acid phytase. © 2017 Society of Chemical Industry.

Boosting Alfalfa (Medicago sativa L.) Production With Rhizobacteria From Various Plants in Saudi Arabia

This study focused on rhizobacteria to promote sustainable crop production in arid regions of Saudi Arabia. The study isolated 17 tightly root-adhering rhizobacteria from various plants at Hada Al Sham in Saudi Arabia. All 17 rhizobacterial isolates were confirmed as plant growth promoting rhizobacteria by classical biochemical tests. Using 16S rDNA gene sequence analyses, the strains were identified as Bacillus, Acinetobacter and Enterobacter. Subsequently, the strains were assessed for their ability to improve the physiology, nutrient uptake, growth, and yield of alfalfa plants grown under desert agriculture conditions. The field trials were conducted in a randomized complete block design. Inoculation of alfalfa with any of these 17 strains improved the relative water content; chlorophyll a; chlorophyll b; carotenoid contents; nitrogen (N), phosphorus, and potassium contents; plant height; leaf-to-stem ratio; and fresh and dry weight. Acinetobacter pittii JD-14 was most effective to increase fresh and dry weight of alfalfa by 41 and 34%, respectively, when compared to non-inoculated control plants. Nevertheless, all strains enhanced crop traits when compared to controls plants, indicating that these desert rhizobacterial strains could be used to develop an eco-friendly biofertilizer for alfalfa and possibly other crop plants to enhance sustainable production in arid regions.

Immobilisation of phytase producing Gluconacetobacter with bacterial cellulose nano‐fibres and promotion of enzyme activities by magnetite nanoparticles

The isolated Gluconacetobacter sp. with accession number: KY996741 was assayed for evaluation of phytase activity. It could solubilise sodium phytate in the absence of soluble phosphate with the cells; however, the enzyme was not seen in cell free extract, to the best of their knowledge the intracellular phytase activities of Gluconacetobacter sp. was not reported previously. Also, the potential of in situ immobilisation of cells produced enzyme (/phytase producing bacteria) in bacterial cellulose was investigated and was studied by SEM and AFM. The results showed that the immobilised probiotic cells had the best activity of 1229 U/ml. The optimum temperature of the immobilised enzyme activity was at 45°C (5969 U/ml) and the immobilised phytase maintained 64% of its activities after two repeated cycles. The enzyme needs mild conditions for its activity and has a short life time and low stability and lost activities from 1229 to 500 U/ml during 30 days. However, it was showed that the addition of 1 ppm nano‐ferric oxide particles could promote the phytase activities of immobilised cell from 500 U/ml to >1500 U/ml. This immobilised phytase producing cells on bacterial cellulose can be useful as food and/feed supplement for phytin removal.

Bacterial impregnation of mineral fertilizers improves yield and nutrient use efficiency of wheat

BACKGROUND

The fertilizer use efficiency (FUE) of agricultural crops is generally low, which results in poor crop yields and low economic benefits to farmers. Among the various approaches used to enhance FUE, impregnation of mineral fertilizers with plant growth-promoting bacteria (PGPB) is attracting worldwide attention. The present study was aimed to improve growth, yield and nutrient use efficiency of wheat by bacterially impregnated mineral fertilizers.

RESULTS

Results of the pot study revealed that impregnation of diammonium phosphate (DAP) and urea with PGPB was helpful in enhancing the growth, yield, photosynthetic rate, nitrogen use efficiency (NUE) and phosphorus use efficiency (PUE) of wheat. However, the plants treated with F8 type DAP and urea, prepared by coating a slurry of PGPB (Bacillus sp. strain KAP6) and compost on DAP and urea granules at the rate of 2.0 g 100 g^-1 fertilizer, produced better results than other fertilizer treatments. In this treatment, growth parameters including plant height, root length, straw yield and root biomass significantly (P ≤ 0.05) increased from 58.8 to 70.0 cm, 41.2 to 50.0 cm, 19.6 to 24.2 g per pot and 1.8 to 2.2 g per pot, respectively. The same treatment improved grain yield of wheat by 20% compared to unimpregnated DAP and urea (F0). Likewise, the maximum increase in photosynthetic rate, grain NP content, grain NP uptake, NUE and PUE of wheat were also recorded with F8 treatment.

CONCLUSION

The results suggest that the application of bacterially impregnated DAP and urea is highly effective for improving growth, yield and FUE of wheat. © 2017 Society of Chemical Industry.

β-Propeller phytases: Diversity, catalytic attributes, current developments and potential biotechnological applications

Phytases are phosphatases which stepwise remove phosphates from phytic acid or its salts. β-Propeller phytase (BPPhy) belongs to a special class of microbial phytases that is regarded as most diverse, isolated and characterized from different microbes, mainly from Bacillus spp. BPPhy class is unique for its Ca²⁺-dependent catalytic activity, strict substrate specificity, active at neutral to alkaline pH and high thermostability. Numerous sequence and structure based studies have revealed unique attributes and catalytic properties of this class, as compared to other classes of phytases. Recent studies including cloning and expression and genetic engineering approaches have led to improvements in BPPhy which provide an opportunity for extended utilization of this class of phytases in improving animal nutrition, human health, plant growth promotion, and environmental protection, etc. This review describes the sources and diversity of BPPhy genes, biochemical properties, Ca²⁺ dependence, current developments in structural elucidation, heterogeneous expression and catalytic improvements, and multifarious applications of BPPhy.

Phylotype Dynamics of Bacterial P Utilization Genes in Microbialites and Bacterioplankton of a Monomictic Endorheic Lake

Microbes can modulate ecosystem function since they harbor a vast genetic potential for biogeochemical cycling. The spatial and temporal dynamics of this genetic diversity should be acknowledged to establish a link between ecosystem function and community structure. In this study, we analyzed the genetic diversity of bacterial phosphorus utilization genes in two microbial assemblages, microbialites and bacterioplankton of Lake Alchichica, a semiclosed (i.e., endorheic) system with marked seasonality that varies in nutrient conditions, temperature, dissolved oxygen, and water column stability. We focused on dissolved organic phosphorus (DOP) utilization gene dynamics during contrasting mixing and stratification periods. Bacterial alkaline phosphatases (phoX and phoD) and alkaline beta-propeller phytases (bpp) were surveyed. DOP utilization genes showed different dynamics evidenced by a marked change within an intra-annual period and a differential circadian pattern of expression. Although Lake Alchichica is a semiclosed system, this dynamic turnover of phylotypes (from lake circulation to stratification) points to a different potential of DOP utilization by the microbial communities within periods. DOP utilization gene dynamics was different among genetic markers and among assemblages (microbialite vs. bacterioplankton). As estimated by the system's P mass balance, P inputs and outputs were similar in magnitude (difference was <10 %). A theoretical estimation of water column P monoesters was used to calculate the potential P fraction that can be remineralized on an annual basis. Overall, bacterial groups including Proteobacteria (Alpha and Gamma) and Bacteroidetes seem to be key participants in DOP utilization responses.

Phytases from Enterobacter and Serratia species with desirable characteristics for food and feed applications

Phytases are enzymes of great industrial importance with wide range of applications in animal and human nutrition. These catalyze the hydrolysis of phosphomonoester bonds in phytate, thereby releasing lower forms of myo-inositol phosphates and inorganic phosphate. Addition of phytase to plant-based foods can improve its nutritional value and increase mineral bioavailability by decreasing nutritional effect of phytate. In the present investigation, 43 phytase positive bacteria on PSM plates were isolated from different sources and characterized for phytase activity. On the basis of phytase activity and zone of hydrolysis, two bacterial isolates (PSB-15 and PSB-45) were selected for further characterization studies, i.e., pH and temperature optima and stability, kinetic properties and effect of modulators. The phytases from both isolates were optimally active at the pH value from 3 to 8 and in the temperature range of 50-70 °C. Further, the stability of isolates was good in the pH range of 3.0-8.0. Much variation was observed in temperature and storage stability, responses of phytases to metal ions and modulators. The K m and V max values for PSB-15 phytase were 0.48 mM and 0.157 μM/min, while for PSB-45 these were 1.25 mM and 0.140 μM/min, respectively. Based on 16S rDNA gene sequence, the isolates were identified as Serratia sp. PSB-15 (GenBank Accession No. KR133277) and Enterobacter cloacae strain PSB-45 (GenBank Accession No. KR133282). The novel phytases from these isolates have multiple characteristics of high thermostability and good phytase activity at desirable range of pH and temperature for their efficient use in food and feed to facilitate hydrolysis of phytate-metal ion complex and in turn, increased bioavailability of important metal ions to monogastric animals.

Novel oligonucleotide primers reveal a high diversity of microbes which drive phosphorous turnover in soil

Phosphorus (P) is of central importance for cellular life but likewise a limiting macronutrient in numerous environments. Certainly microorganisms have proven their ability to increase the phosphorus bioavailability by mineralization of organic-P and solubilization of inorganic-P. On the other hand they efficiently take up P and compete with other biota for phosphorus. However the actual microbial community that is associated to the turnover of this crucial macronutrient in different ecosystems remains largely anonymous especially taking effects of seasonality and spatial heterogeneity into account. In this study seven oligonucleotide primers are presented which target genes coding for microbial acid and alkaline phosphatases (phoN, phoD), phytases (appA), phosphonatases (phnX) as well as the quinoprotein glucose dehydrogenase (gcd) and different P transporters (pitA, pstS). Illumina amplicon sequencing of soil genomic DNA underlined the high rate of primer specificity towards the respective target gene which usually ranged between 98% and 100% (phoN: 87%). As expected the primers amplified genes from a broad diversity of distinct microorganisms. Using DNA from a beech dominated forest soil, the highest microbial diversity was detected for the alkaline phosphatase (phoD) gene which was amplified from 15 distinct phyla respectively 81 families. Noteworthy the primers also allowed amplification of phoD from 6 fungal orders. The genes coding for acid phosphatase (phoN) and the quinoprotein glucose dehydrogenase (gcd) were amplified from 20 respectively 17 different microbial orders. In comparison the phytase and phosphonatase (appA, phnX) primers covered 13 bacterial orders from 2 different phyla respectively. Although the amplified microbial diversity was apparently limited both primers reliably detected all orders that contributed to the P turnover in the investigated soil as revealed by a previous metagenomic approach. Genes that code for microbial P transporter (pitA, pstS) were amplified from 13 respectively 9 distinct microbial orders. Accordingly the introduced primers represent a valuable tool for further analysis of the microbial community involved in the turnover of phosphorus in soils but most likely also in other environments.

A novel phytase characterized by thermostability and high pH tolerance from rice phyllosphere isolated Bacillus subtilis B.S.46

In this study, an extracellular alkali-thermostable phytase producing bacteria, Bacillus subtilis B.S.46, were isolated and molecularly identified using 16S rRNA sequencing. Response surface methodology was applied to study the interaction effects of assay conditions to obtain optimum value for maximizing phytase activity. The optimization resulted in 137% (4.627 U/mL) increase in phytase activity under optimum condition (56.5 °C, pH 7.30 and 2.05 mM sodium phytate). The enzyme also showed 60-73% of maximum activity at wide ranges of temperature (47-68 °C), pH (6.3-8.0) and phytate concentration (1.40-2.50 mM). The partially purified phytase demonstrated high stability over a wide range of pH (6.0-10.0) after 24 h, retaining 85% of its initial activity at pH 6 and even interestingly, the phytase activity enhanced at pH 8.0-10.0. It also exhibited thermostability, retaining about 60% of its original activity after 2 h at 60 °C. Cations such as Ca(2+) and Li(+) enhanced the phytase activity by 10-46% at 1 mM concentration. The phytase activity was completely inhibited by Cu(2+), Mg(2+), Fe(2+), Zn(2+), Hg(2+) and Mn(2+) and the inhibition was in a dose dependent manner. B. subtilis B.S.46 phytase had interesting characteristics to be considered as animal feed additive, dephytinization of food ingredients, and bioremediation of phosphorous pollution in the environment.