Microbial phytases in phosphorus acquisition and plant growth promotion

Inoculation with Bacillus megaterium CNPMS B119 and Bacillus subtilis CNPMS B2084 improve P-acquisition and maize yield in Brazil

Phosphorus (P) is a critical nutrient for plant growth, yet its uptake is often hindered by soil factors like clay minerals and metal oxides such as aluminum (Al), iron (Fe), and calcium (Ca), which bind P and limit its availability. Phosphate-solubilizing bacteria (PSB) have the unique ability to convert insoluble P into a soluble form, thereby fostering plant growth. This study aimed to assess the efficacy of inoculation of Bacillus megaterium B119 (rhizospheric) and B. subtilis B2084 (endophytic) via seed treatment in enhancing maize yield, grain P content, and enzyme activities across two distinct soil types in field conditions. Additionally, we investigated various mechanisms contributing to plant growth promotion, compatibility with commercial inoculants, and the maize root adhesion profile of these strains. During five crop seasons in two experimental areas in Brazil, Sete Lagoas-MG and Santo Antônio de Goiás-GO, single inoculations with either B119 or B2084 were implemented in three seasons, while a co-inoculation with both strains was applied in two seasons. All treatments received P fertilizer according to plot recommendations, except for control. Both the Bacillus strains exhibited plant growth-promoting properties relevant to P dynamics, including phosphate solubilization and mineralization, production of indole-3-acetic acid (IAA)-like molecules, siderophores, exopolysaccharides (EPS), biofilms, and phosphatases, with no antagonism observed with Azospirillum and Bradyrizhobium. Strain B2084 displayed superior maize root adhesion compared to B119. In field trials, single inoculations with either B119 or B2084 resulted in increased maize grain yield, with relative average productivities of 22 and 16% in Sete Lagoas and 6 and 3% in Santo Antônio de Goiás, respectively. Co-inoculation proved more effective, with an average yield increase of 24% in Sete Lagoas and 11% in Santo Antônio de Goiás compared to the non-inoculated control. Across all seasons, accumulated grain P content correlated with yield, and soil P availability in the rhizosphere increased after co-inoculation in Santo Antônio de Goiás. These findings complement previous research efforts and have led to the validation and registration of the first Brazilian inoculant formulated with Bacillus strains for maize, effectively enhancing and P grain content.

Soil chemical fumigation alters soil phosphorus cycling: effects and potential mechanisms

Soil chemical fumigation is an effective and popular method to increase agricultural productivity. However, the broad-spectrum bioactivity of fumigants causes harm to soil beneficial microorganisms involved in the soil phosphorous cycle, such as soil phosphorus solubilizing microorganisms (PSMs). We review the effects of soil chemical fumigation on soil phosphorus cycling, and the potential underlying mechanisms that ultimately lead to altered phosphorus availability for crops. These complex processes involve the highly diverse PSM community and a plethora of soil phosphorus forms. We discuss phosphatizing amendments aimed at counteracting the possible negative effects of fumigation on phosphorus availability, phosphorus use efficiency, and crop yields. We also emphasize distinguishing between the effects on soil phosphorus cycling caused by the chemical fumigants, and those caused by the fumigation process (e.g. plastic mulching). These are typically conflated in the literature; distinguishing them is critical for identifying appropriate amendments to remediate possible post-fumigation soil phosphorus deficiencies.

Organic phosphorus levels change the hyphosphere phoD-harboring bacterial community of Funneliformis mosseae

The phoD-harboring bacterial community is responsible for organic phosphorus (P) mineralization in soil and is important for understanding the interactions between arbuscular mycorrhizal (AM) fungi and phosphate-solubilizing bacteria (PSB) at the community level for organic P turnover. However, current understanding of the phoD-harboring bacterial community associated with AM fungal hyphae responses to organic P levels remains incomplete. Here, two-compartment microcosms were used to explore the response of the phoD-harboring bacterial community in the hyphosphere to organic P levels by high-throughput sequencing. Extraradical hyphae of Funneliformis mosseae enriched the phoD-harboring bacterial community and organic P levels significantly altered the composition of the phoD-harboring bacterial community in the Funneliformis mosseae hyphosphere. The relative abundance of dominant families Pseudomonadaceae and Burkholderiaceae was significantly different among organic P treatments and were positively correlated with alkaline phosphatase activity and available P concentration in the hyphosphere. Furthermore, phytin addition significantly decreased the abundance of the phoD gene, and the latter was significantly and negatively correlated with available P concentration. These findings not only improve the understanding of how organic P influences the phoD-harboring bacterial community but also provide a new insight into AM fungus-PSB interactions at the community level to drive organic P turnover in soil.

Bacterial community structure and co-occurrence networks in the rhizosphere and root endosphere of the grafted apple

BACKGROUND

Compared with aerial plant tissues (such as leaf, stem, and flower), root-associated microbiomes play an indisputable role in promoting plant health and productivity. We thus explored the similarities and differences between rhizosphere and root endosphere bacterial community in the grafted apple system.

RESULTS

Using pot experiments, three microhabitats (bulk soil, rhizosphere and root endosphere) samples were obtained from two-year-old apple trees grafted on the four different rootstocks. We then investigated the bacterial community composition, diversity, and co-occurrence network in three microhabitats using the Illumina sequencing methods. Only 63 amplicon sequence variants (ASVs) out of a total of 24,485 were shared in the rhizosphere and root endosphere of apple grafted on the four different rootstocks (M9T337, Malus hupehensis Rehd., Malus robusta Rehd., and Malus baccata Borkh.). The core microbiome contained 8 phyla and 25 families. From the bulk soil to the rhizosphere to the root endosphere, the members of the phylum and class levels demonstrated a significant enrichment and depletion pattern. Co-occurrence network analysis showed the network complexity of the rhizosphere was higher than the root endosphere. Most of the keystone nodes in both networks were classified as Proteobacteria, Actinobacteriota and Bacteroidetes and were low abundance species.

CONCLUSION

The hierarchical filtration pattern existed not only in the assembly of root endosphere bacteria, but also in the core microbiome. Moreover, most of the core ASVs were high-abundance species, while the keystone ASVs of the network were low-abundance species.

Production of fungal phytases in solid state fermentation and potential biotechnological applications

Phytases are important enzymes used for eliminating the anti-nutritional properties of phytic acid in food and feed ingredients. Phytic acid is major form of organic phosphorus stored during seed setting. Monogastric animals cannot utilize this phytate-phosphorus due to lack of necessary enzymes. Therefore, phytic acid excretion is responsible for mineral deficiency and phosphorus pollution. Phytases have been reported from diverse microorganisms, however, fungal phytases are preferred due to their unique properties. Aspergillus species are the predominant producers of phytases and have been explored widely as compared to other fungi. Solid-state fermentation has been studied as an economical process for the production of phytases to utilize various agro-industrial residues. Mixed substrate fermentation has also been reported for the production of phytases. Physical and chemical parameters including pH, temperature, and concentrations of media components have significantly affected the production of phytases in solid state fermentation. Fungi produced high levels of phytases in solid state fermentation utilizing economical substrates. Optimization of culture conditions using different approaches has significantly improved the production of phytases. Fungal phytases are histidine acid phosphatases exhibiting broad substrate specificity, are relatively thermostable and protease-resistant. These phytases have been found effective in dephytinization of food and feed samples with concomitant liberation of minerals, sugars and soluble proteins. Additionally, they have improved the growth of plants by increasing the availability of phosphorus and other minerals. Furthermore, phytases from fungi have played an important roles in bread making, semi-synthesis of peroxidase, biofuel production, production of myo-inositol phosphates and management of environmental pollution. This review article describes the production of fungal phytases in solid state fermentation and their biotechnological applications.

Microbial Phytases: Properties and Applications in the Food Industry

Microbial phytases are enzymes that break down phytic acid, an anti-nutritional compound found in plant-based foods. These enzymes which are derived from bacteria and fungi have diverse properties and can function under different pH and temperature conditions. Their ability to convert phytic acid into inositol and inorganic phosphate makes them valuable in food processing. The application of microbial phytases in the food industry has several advantages. Firstly, adding them to animal feedstuff improves phosphorus availability, leading to improved nutrient utilization and growth in animals. This also reduces environmental pollution by phosphorus from animal waste. Secondly, microbial phytases enhance mineral bioavailability and nutrient assimilation in plant-based food products, counteracting the negative effects of phytic acid on human health. They can also improve the taste and functional properties of food and release bioactive compounds that have beneficial health effects. To effectively use microbial phytases in the food industry, factors like enzyme production, purification, and immobilization techniques are important. Genetic engineering and protein engineering have enabled the development of phytases with improved properties such as enhanced stability, substrate specificity, and resistance to degradation. This review provides an overview of the properties and function of phytases, the microbial strains that produce them, and their industrial applications, focusing on new approaches.

Phosphorus quantification in soil using LIBS assisted by laser-induced fluorescence

Quantification and monitoring of phosphorus in soil plays a critical role in environmentally friendly agriculture, especially in mitigation of phosphorus leakages to water systems and subsequent risk for eutrophication. On the other hand, deficiency in phosphorus would lead to problems in development and growth of cultivated crops. Therefore, monitoring and quantification of phosphorus status in soil is essential. In this work, laser-induced breakdown spectroscopy assisted by laser-induced fluorescence (LIBS-LIF) is introduced for quantification of readily soluble phosphorus in soil and compared to the analytical performance of the conventional LIBS method. Mineral soils with variable phosphorus status were used for the analysis. The calibration curves are plotted to evaluate the detection limit of the soluble phosphorus. Compared results demonstrate improvement in detection limit from 3.74 mg/kg to 0.12 mg/kg for clay soil and from 10.94 mg/kg to 0.27 mg/kg for silt loam/loam soil in LIBS and LIBS-LIF measurements, respectively. For the LIBS-LIF measurement, detection limits are comparable with established chemical soil analyses. The proposed method would substantially reduce required sample preparation and laboratory work compared with conventional phosphorus quantification. In addition, as the calibration curves demonstrate that the calibration for soluble phosphorus holds within a soil type, LIBS-LIF has the potential to be used for high throughput soil analysis.

Characterization of 5'-nucleotidases secreted from Streptomyces

To study the ability of Streptomyces to utilize environmental nucleotides, we screened for strains exhibiting extracellular 5'-inosine monophosphate (IMP)-dephosphorylating activity in our collection of soil isolates and obtained two producers: NE5-10 and Y2F8-2. The enzyme responsible for the activity was purified from the culture supernatant of each strain, and its mass spectral data were used to identify the coding sequence. The gene was successfully identified in the whole genome sequence of each strain; it was located in a conserved gene cluster of phosphate-related functions and encoded an approximately 600-amino acid long protein containing an N-terminal secretion signal. The mature part of the protein exhibited similarity to a known bacterial 5'-nucleotidase. The locus of the 5'-nucleotidase gene contained genes encoding proteins involved in phosphate utilization. The conserved gene arrangement of the locus in various Streptomyces genomes suggested the genetic region to be involved in phosphate-scavenging in this group of bacteria. Phylogenetic analysis demonstrated that the isolated Streptomyces enzymes represent an uncharacterized group of bacterial 5'-nucleotidases. Enzymatic characterization of the two Streptomyces enzymes demonstrated that both enzymes exhibited 5'-nucleotidase activity but differed in terms of optimal temperature and pH, dependence on divalent cations, and substrate specificity. The Km and Vmax values of the 5'-IMP-dephosphorylating activity were 0.239 mM and 9.47 U/mg, respectively, for NE5-10 and 0.221 mM and 38.17 U/mg, respectively, for Y2F8-2. Enzyme activity in the culture broth of the two Streptomyces producers occurred in a phosphate-limitation-dependent manner, supporting their involvement in the acquisition of phosphorus. KEY POINTS: • We purified and characterized nucleotidases from two Streptomyces. • Two nucleotidases were presumed to be involved in phosphate acquisition. • It showed diversity in phosphate acquisition among microorganisms.

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.

Apple Endophytic fungi and their antagonism against apple scab disease

Endophytic fungi are microorganisms with the ability to colonize plants for the entire or at least a significant part of their life cycle asymptomatically, establishing a plant-fungus association. They play an important role in balancing ecosystems, as well as benefiting host through increasing plant growth, and protecting the host plants from abiotic and biotic stresses using various strategies. In the present study, endophytic fungi were isolated from wild and endemic apple cultivars, followed by characterizing their antifungal effect against Venturia inaequalis. To characterize the endophytic fungi, 417 fungal strains were separated from 210 healthy fruit, leaf, and branch samples collected from the north of Iran. Among the purified fungal isolates, 33 fungal genera were identified based on the morphological characteristics, of which 38 species were detected according to the morphological features and molecular data of ITS, tef-1α, and gapdh genomic regions (related to the genus). The results represented that most of the endophytic fungi belonged to Ascomycota (67.8%), 31.4% of isolates were mycelia sterilia, while the others were Basidiomycota (0.48%) and Mucoromycota (0.24%). Additionally, Alternaria, Cladosporium, and Nigrospora were determined as the dominant genera. The antifungal properties of the identified isolates were evaluated against V. inaequalis in vitro to determine the release of media-permeable metabolites, Volatile Organic Compounds (VOCs), chitinase, and cellulase as antifungal mechanisms, as well as producing phosphate solubilisation as growth-promoting effect. Based on the results of metabolite and VOC tests, the six isolates of Acremonium sclerotigenum GO13S1, Coniochaeta endophytica 55S2, Fusarium lateritium 61S2, Aureobasidium microstictum 7F2, Chaetomium globosum 2S1 and Ch. globosum 3 L2 were selected for greenhouse tests. Further, Co. endophytica 55S2 and F. lateritium 61S2 could solubilize inorganic phosphate. All isolates except Ch. globosum 3 L2 exhibited cellulase activity, while chitinase activity was observed in Ch. globosum 2S1, Ch. globosum 3 L2, and F. lateritium 61S2. Finally, Co. endophytica 55S2 and Ch. globosum 2S1 completely controlled the disease on the apple seedling leaves under greenhouse conditions.

Impacts and Industrial Applications of Phytic Acid and Phytase

Phytic acid is an antinutritional compound that chelates P and essential divalent cations such as Fe, Ca, and Zn in cereals and major staple crops such as wheat, maize, rice, and sorghum. As a result, these cations cannot be absorbed by monogastric animals or humans: phytic acid has an inhibitory effect on nutrient uptake and its levels are negatively correlated with protein and starch digestibility. However, phytic acid can be degraded by the action of the enzyme phytase. Phytase plays important roles in the degradation of phytic acid and in increasing the nutritional quality of staple foods. Microbial phytase is a versatile enzyme that is beneficial for humans, animals, the environment, and the industry. In this review, we summarise the interaction of phytic acid with micronutrients, various approaches to enhancing the nutritional profile of staple foods by reducing the phytic acid content, and current knowledge of microbial-based phytase as a potential reducer of phytic acid.

Responses of invasive and native plants to different forms and availability of phosphorus

PREMISE

Many studies have assessed the various responses of alien plants to changes in overall nutrient or different nitrogen (N) availabilities. However, in natural soils, nutrients are present as different elements (e.g., N and phosphorus [P]) and forms (e.g., inorganic and organic). Few studies have explored whether invasive and native species differ in their responses to varying P availability and forms.

METHODS

We grew five taxonomically related pairs of common herbaceous, invasive and native species alone or in competition under six different conditions of P availability or forms and assessed their growth performance.

RESULTS

Invasive species overall did not produce more biomass than native species did in the various P conditions. However, the biomass response to organic forms of P was, relative to the response to inorganic forms of P, stronger for the invasive species than that for the native species and agreed with invasive species mainly allocating biomass to the root system under organic P conditions.

CONCLUSIONS

While invasive species were not more promiscuous than the native species, they took great advantage of the organic P forms. Therefore, the invasion risk of alien species may increase in habitats with more organic P sources.

Fluorometric detection of phytase enzyme activity and phosphate ion based on gelatin supported silver nanoclusters

Phytase is the commercial enzyme for bioconversion of phytate substrate to digestible phosphate ions. Recently silver nanoclusters (AgNCs) have received great attention as the optical transducer nanoparticles in biosensors structure. The novel detection platform was developed to detect the phytase enzyme activity and phosphate ions based on fluorescence quenching of AgNCs. The AgNCs were synthesized through gelatin supported reaction and characterized by TEM, FTIR and XRD analysis. The hydrolytic effect of phytase enzyme and subsequent phosphate release led to suppression of AgNCs fluorescence. The linear range was observed for enzyme in the range of 0.5-5 U/mL with the detection limit of 0.2 U/mL. Also, the same fluorescence quenching effect was observed in the presence of phosphate ion in the linear range of 1 to 16 µM with a detection limit of 0.5 µM. The proposed mechanism showed effectiveness of detection strategy for detection of phytase enzyme and phosphate ion.

Impact of phosphorous-deficit conditions on morpho-physiological traits and phosphorous metabolism in chickpea genotypes

Chickpea, an important food legume, is primarily grown on marginal soils with low soil fertility. Although chickpea can fix N, soil phosphorus (P) deficiency in crop growing areas is a major limiting factor for chickpea production. This study was undertaken to evaluate twenty-five chickpea cultivars for morpho-physiological traits and yield under low and normal phosphorous conditions. Based on morpho-physiological traits such as length and area of roots and shoots, root length density, root and shoot biomass, chlorophyll content, number of nodules and root tips, tolerance indices and yield, these cultivars were characterised into susceptible (ICC67, ICC1915, ICC2593, ICC5337, ICC5879, ICC8950, ICC13441, ICC1483, ICC15606 and ICC15888), tolerant (ICC10755, IG72070, ICCV97105, ICCV2, ICCV92809, ICCV92337 and ICCV95423) and the remaining cultivars were moderately tolerant to phosphorous-deficit conditions. Higher activities of enzymes of phosphorous metabolism such as acid phosphatase and phytase in roots and nodules of tolerant chickpea cultivars (ICCV97105, ICCV92337, ICCV95423) as compared to susceptible cultivars (ICC67, ICC15606, ICC15888) at different developmental stages might be attributing to their better performance for growth parameters and productivity traits under phosphorous-deficit conditions.

Tobacco Plant Growth-Promoting and Antifungal Activities of Three Endophytic Yeast Strains

In this research, the biosynthetic and biocontrol potential of endophytic yeast to improve the growth and development of tobacco has been elucidated. Three yeast strains were enriched and isolated from different plant tissues. Partial sequence analysis of ITS5-5.8-ITS4 region of the nuclear ribosomal DNA with universal primers identified YD5, YE1, and YSW1 as Saccharomyces cerevisiae (S. cerevisiae), Zygosaccharomyces bailii (Z. bailii), and Saccharomyces kudriavzevii (S. kudriavzevii), respectively. When cultivated in a medium supplemented with 0.1% L-tryptophan, isolated yeast strains produced indole-3-acetic acid (IAA). The capacities of those strains to improve the mobility of phosphorus and synthesize siderophores has been proven. Their antimicrobial activities against several Solanaceae plant pathogenic fungi (Alternaria solani pathovar. tobacco, Rhizoctonia solani, and Fusarium solani pathovar. phaseoli) were determined. S. cerevisiae YD5, Z. bailii YE1, and S. kudriavzevii YSW1 inhibited the growth of all tested pathogens. Yeast strains were tested for endophytic colonization of tobacco by two different inoculation methods: soil drench (SD) and leaf spraying (LS). To establish colonization in the various tissues of tested tobacco (Nicotiana tabaccum L.) plants, samples were taken on the seventh, fourteenth, and twenty-first days after treatment (DAT), and explants were inoculated on yeast malt agar (YMA). Both techniques of inoculation showed a high frequency of colonization from 83.33% to 100%. To determine the effectiveness of the microbial endophytes, their effect on some physiological processes in the plant were analyzed, such as photosynthesis, stomatal conductivity, and transpiration intensity. The effect of single and double treatment with yeast inoculum on the development and biochemical parameters of tobacco was reported. Plants have the ability of structural and functional adaptation to stress effects of different natures. All treated plants had a higher content of photosynthetic pigments compared to the control. Photosynthesis is probably more intense, and growth stimulation has been observed. The chlorophyll a/b ratio remained similar, and the total chlorophyll/carotenoid ratio slightly increased as a result of elevated chlorophyll levels. The most significant stimulating effect was recorded in tobacco plants treated by foliar spraying with Z. bailii YE1 and S. cerevisiae YD5. In contrast, S. kudriavzevii YSW1 had a better effect when applied as a soil drench. Thus, S. cerevisiae YD5, Z. bailii YE1, and S. kudriavzevii YSW1 have a high potential to be used as a biocontrol agents in organic agriculture.

Functional Genetic Diversity and Plant Growth Promoting Potential of Polyphosphate Accumulating Bacteria in Soil

Polyphosphate (polyP) accumulation is an important trait of microorganisms. Implication of polyP accumulating bacteria (PAB) in enhanced biological phosphate removal, heavy metal sequestration, and dissolution of dental enamel is well studied. Phosphorous (P) accumulated within microbial biomass also regulates labile P in soil; however, abundance and diversity of the PAB in soil is still unexplored. Present study investigated the genetic and functional diversity of PAB in rhizosphere soil. Here, we report the abundance of Pseudomonas spp. as high PAB in soil, suggesting their contribution to global P cycling. Additional subset analysis of functional genes i.e., polyphosphate kinase (ppk) and exopolyphosphatase (ppx) in all PAB, indicates their significance in bacterial growth and metabolism. Distribution of functional genes in phylogenetic tree represent a more biologically realistic discrimination for the two genes. Distribution of ppx gene disclosed its phylogenetic conservation at species level, however, clustering of ppk gene of similar species in different clades illustrated its environmental condition mediated modifications. Selected PAB showed tolerance to abiotic stress and strong correlation with plant growth promotary (PGP) traits viz. phosphate solubilization, auxin and siderophore production. Interaction of PAB with A. thaliana enhanced the growth and phosphate status of the plant under salinity stress, suggestive of their importance in P cycling and stress alleviation.

IMPORTANCE Study discovered the abundance of Pseudomonas genera as a high phosphate accumulator in soil. The presence of functional genes (polyphosphate kinase [ppk] and exopolyphosphatase [ppx]) in all PAB depicts their importance in polyphosphate metabolism in bacteria. Genetic and functional diversity reveals conservation of the ppx gene at species level. Furthermore, we found a positive correlation between PAB and plant growth promotary traits, stress tolerance, and salinity stress alleviation in A. thaliana.

Perception of Biocontrol Potential of Bacillus inaquosorum KR2-7 against Tomato Fusarium Wilt through Merging Genome Mining with Chemical Analysis

Simple Summary

Bacillus is a bacterial genus that is widely used as a promising alternative to chemical pesticides due to its protective activity toward economically important plant pathogens. Fusarium wilt of tomato is a serious fungal disease limiting tomato production worldwide. Recently, the newly isolated B. inaquosorum strain KR2-7 considerably suppressed Fusarium wilt of tomato plants. The present study was performed to perceive potential direct and indirect biocontrol mechanisms implemented by KR2-7 against this disease through genome and chemical analysis. The potential direct biocontrol mechanisms of KR2-7 were determined through the identification of genes involved in the synthesis of antibiotically active compounds suppressing tomato Fusarium wilt. Furthermore, the indirect mechanisms of this bacterium were perceived through recognizing genes that contributed to the resource acquisition or modulation of plant hormone levels. This is the first study that aimed at the modes of actions of B. inaquosorum against Fusarium wilt of tomatoes and the results strongly indicate that strain KR2-7 could be a good candidate for microbial biopesticide formulations to be used for biological control of plant diseases and plant growth promotion.

Abstract

Tomato Fusarium wilt, caused by Fusarium oxysporum f. sp. lycopersici (Fol), is a destructive disease that threatens the agricultural production of tomatoes. In the present study, the biocontrol potential of strain KR2-7 against Fol was investigated through integrated genome mining and chemical analysis. Strain KR2-7 was identified as B. inaquosorum based on phylogenetic analysis. Through the genome mining of strain KR2-7, we identified nine antifungal and antibacterial compound biosynthetic gene clusters (BGCs) including fengycin, surfactin and Bacillomycin F, bacillaene, macrolactin, sporulation killing factor (skf), subtilosin A, bacilysin, and bacillibactin. The corresponding compounds were confirmed through MALDI-TOF-MS chemical analysis. The gene/gene clusters involved in plant colonization, plant growth promotion, and induced systemic resistance were also identified in the KR2-7 genome, and their related secondary metabolites were detected. In light of these results, the biocontrol potential of strain KR2-7 against tomato Fusarium wilt was identified. This study highlights the potential to use strain KR2-7 as a plant-growth promotion agent.

Plant Growth Promotion at Low Temperature by Phosphate-Solubilizing Pseudomonas Spp. Isolated from High-Altitude Himalayan Soil

Scarcity of arable land, limited soil nutrient availability, and low-temperature conditions in the Himalayan regions need to be smartly managed using sustainable approaches for better crop yields. Microorganisms, able to efficiently solubilize phosphate at low temperatures, provide an opportunity to promote plant growth in an ecofriendly way. In this study, we have investigated the ability of psychrotolerant Pseudomonas spp., isolated from high altitudes of Indian Himalaya to solubilize P at low temperature. Quantitative estimation of phosphate solubilization and production of relevant enzymes at two different temperatures (15 and 25 °C) was performed for 4 out of 11 selected isolates, namely, GBPI_506 (Pseudomonas sp.), GBPI_508 (Pseudomonas palleroniana), GBPI_Hb61 (Pseudomonas proteolytica), and GBPI_CDB143 (Pseudomonas azotoformans). Among all, isolate GBPI_CDB143 showed highest efficiency to solubilize tri-calcium phosphate (110.50 ± 3.44 μg/mL) at 25 °C after 6 days while the culture supernatants of isolate GBPI_506 displayed the highest phytase activity (15.91 ± 0.35 U/mL) at 15 °C and alkaline phosphatase (3.09 ± 0.07 U/mL) at 25 °C in 6 and 9 days, respectively. Out of five different organic acids quantified, oxalic acid and malic acid were produced in maximum quantity by all four isolates. With the exception of GBPI_508, inoculation of bacteria promoted overall growth (rosette diameter, leaf area, and biomass) of Arabidopsis thaliana plants as compared to uninoculated control plants in growth chamber conditions. The plant growth promotion by each bacterial isolate was further validated by monitoring root colonization in the inoculated plants. These bacterial isolates with low-temperature phosphate solubilization potential along with phosphatases and phytase activity at low temperature could be harnessed for sustainable crop production in P-deficient agricultural soils under mountain ecosystems.

The Effects of Host Plant Genotype and Environmental Conditions on Fungal Community Composition and Phosphorus Solubilization in Willow Short Rotation Coppice

Phosphorus (P) is an essential plant nutrient. Low availability of P in soil is mainly caused by high content of Fe2O3 in the clay fraction that binds to P making it unavailable. Beneficial microbes, such as P solubilizing microorganisms can increase the available P in soil and improve plant growth and productivity. In this study, we evaluated the effects of environmental conditions (climate, soil parameters), plant genotype, and level of plant association (rhizosphere or endophytic root organism) on the abundance and diversity of phosphorus solubilizing microorganisms in a Salix production system. We hypothesized that a lower number of endophytic fungi may possess the ability to solubilize P compared to the number of rhizosphere fungi with the same ability. We also expect that the plant genotype and the experimental site with its environmental conditions will influence fungal diversity. Two Salix genotypes grown in pure and mixed cultures were investigated for their fungal microbiome community and diversity in the rhizosphere and endosphere during two growing seasons. We found that the rhizosphere fungal community was more diverse. A general dominance of Ascomycota (Dothideomycetes) and Basidiomycota (Tremellomycetes) was observed. The classes Agaricomycetes and Pezizomycetes were more frequent in the endosphere, while Tremellomycetes and Mortierellomycetes were more abundant in the rhizosphere. Plot-specific soil properties (pH, total organic carbon, and nitrogen) significantly influenced the fungal community structure. Among the culturable fungal diversities, 10 strains of phosphate solubilizing fungi (PSFs) from roots and 12 strains from rhizosphere soil were identified using selective media supplemented with di-calcium and tri-calcium phosphates. The fungal density and the number of PSF were much higher in the rhizosphere than in the endosphere. Penicillium was the dominant genus of PSF isolated from both sites; other less frequent genera of PSFs were Alternaria, Cladosporium, and Clonostachys. Overall the main factors controlling the fungal communities (endophytic vs. rhizosphere fungi) were the soil properties and level of plant association, while no significant influence of growing season was observed. Differences between Salix genotypes were observed for culturable fungal diversity, while in metagenomic data analysis, only the class Dothideomycetes showed a significant effect from the plant genotype.

Effect of Solid-State Fermentation on Nutritional Quality of Leaf Flour of the Drumstick Tree (Moringa oleifera Lam.)

The drumstick tree is a fast-growing multipurpose tree with a large biomass and high nutritional value. However, it has rarely been exploited as a protein source. This study investigated solid-state fermentation induced by Aspergillus niger, Candida utilis and Bacillus subtilis to obtain high-quality protein feed from drumstick leaf flour. The results showed that fermentation induced significant changes in the nutritional composition of drumstick leaf flour. The concentrations of crude protein, small peptides and amino acids increased significantly after fermentation. The protein profile was also affected by the fermentation process. Macromolecular proteins in drumstick leaf flour were degraded, whereas other high molecular weight proteins were increased. However, the concentrations of crude fat, fiber, total sugar and reducing sugar were decreased, as were the anti-nutritional factors tannins, phytic acid and glucosinolates. After 24 h fermentation, the concentrations of total phenolics and flavonoids were increased. The antioxidant capacity was also significantly enhanced.

Plant growth-promoting potential of 'Myroides gitamensis' isolated from virgin soils of Punjab

Phosphate-solubilizing (PS) and phosphate-mineralizing (PM) bacteria are considered vital for augmenting the plant growth through phosphorus mobilization and plant growth-promoting attributes. In the present study, a rhizospheric bacterium was isolated from the virgin land of Punjab, India and identified as 'Myroides gitamensis' BSH-3 through 16S rRNA sequencing. 'M. gitamensis' showed potential halo zone on Pikovskaya agar. The novelty of the study lies in the fact that plant growth-promoting potential of 'M. gitamensis' has not been studied earlier. It was able to solubilize 17.53-106.66 µg/mL of tricalcium phosphate and demonstrated a promising potential of mineralizing sodium phytate corresponding to 44.6-94.70 µg/mL at 28 °C. Variable PS and PM activity was observed at temperature range of 15-42 °C with the maximum activity observed at 28 °C after 96 h of incubation. The nitrogen fixation ability, hydrogen sulfide production, cellulose hydrolysis test and chitin degradation was found to be negative. High indole acetic acid (42.82 µg/mL), gibberellic acid (72.93 µg/mL), ammonia (22.58 µg/mL) production, phytase activity (0.49 pi/mL/min) and comparable amount of siderophore (28.55%) and acid phosphate activity (0.606 µM p-nitrophenol/ml/min) was shown by 'M. gitamensis'. Inoculation of wheat with 'M. gitamensis' in pot experiment showed increased shoot and root length by 30.58% and 38.32%. Fresh weight and dry weight was increased by 45.74% and 67.81%, respectively, compared to uninoculated control. These results demonstrate that 'M. gitamensis' has promising PS, PM and plant growth-promoting attributes to be used as a bio-inoculant to enhance plant growth and soil fertility.

Hierarchical Reactivity of Enzyme-Mediated Phosphorus Recycling from Organic Mixtures by Aspergillus niger Phytase

Biological recycling of inorganic phosphorus (P_i) from organic phosphorus (P_o) compounds by phosphatase-type enzymes, including phytases, is an important contributor to the pool of bioavailable P to plants and microorganisms. However, studies of mixed-substrate reactions with these enzymes are lacking. Here, we explore the reactivity of a phytase extract from the fungus Aspergillus niger toward a heterogeneous mixture containing, in addition to phytate, different structures of environmentally relevant P_o compounds such as ribonucleotides and sugar phosphates. Using a high-resolution liquid chromatography-mass spectrometry method to monitor simultaneously the parent P_o compounds and their by-products, we captured sequential substrate-specific evolution of P_i from the mixture, with faster hydrolysis of multiphosphorylated compounds (phytate, diphosphorylated sugars, and di- and tri-phosphorylated ribonucleotides) than hydrolysis of monophosphorylated compounds (monophosphorylated sugars and monophosphorylated ribonucleotides). The interaction mechanisms and energies revealed by molecular docking simulations of each P_o compound within the enzyme's active site explained the substrate hierarchy observed experimentally. Specifically, the favorable orientation for binding of the negatively charged phosphate moieties with respect to the positive potential surface of the active site was important. Collectively, our findings provide mechanistic insights about the broad but hierarchical role of phytase-type enzymes in P_i recycling from the heterogeneous assembly of P_o compounds in agricultural soils or wastes.

Impacts of replanting American ginseng on fungal assembly and abundance in response to disease outbreaks

Soil physicochemical properties and fungal communities are pivotal factors for continuous cropping of American ginseng (Panax quinquefolium L.). However, the response of soil physicochemical properties and fungal communities to replant disease of American ginseng has not yet been studied. High-throughput sequencing and soil physicochemical analyses were undertaken to investigate the difference of soil fungal communities and environmental driver factors in new and old ginseng fields; the extent of replant disease in old ginseng fields closely related to changes in soil properties and fungal communities was also determined. Results indicated that fungal communities in an old ginseng field were more sensitive to the soil environment than those in a new ginseng field, and fungal communities were mainly driven by soil organic matter (SOM), soil available phosphorus (AP), and available potassium (AK). Notably, healthy ginseng plants in new and old ginseng fields may influence fungal communities by actively recruiting potential disease suppressive fungal agents such as Amphinema, Cladophialophora, Cadophora, Mortierella, and Wilcoxina. When these key groups and members were depleted, suppressive agents in the soil possibly declined, increasing the abundance of pathogens. Soil used to grow American ginseng in the old ginseng field contained a variety of fungal pathogens, including Alternaria, Armillaria, Aphanoascus, Aspergillus, Setophoma, and Rhexocercosporidium. Additionally, micro-ecological factors affecting disease outbreaks in the old ginseng field included a strengthening in competition relationships, a weakening in cooperation relationships, and a change of trophic strategies among fungal communities.

Solid state fermentation of Moringa oleifera leaf meal by mixed strains for the protein enrichment and the improvement of nutritional value

Moringa oleifera Lam. (MO) is a fast-growing multi-purpose deciduous tree with high biomass and nutritional value. However, the presence of antinutritional factors, poor palatability, and indigestibility of Moringa oleifera leaf meal (MOLM) restrict its application to animal feed. This study aimed to obtain high-quality protein feeds via solid-state fermentation (SSF) of MOLM. The process conditions for increasing the true protein (TP) content using Aspergillus niger, Candida utilis and Bacillus subtilis co-cultures were optimized, and the chemical composition of MOLM was compared before and after fermentation. The results of this study showed that the highest TP content could be obtained through mixed-strain culture of A. niger, C. utilis and B. subtilis at a ratio of 1:1:2. The MOLM was inoculated with A. niger, followed by C. utilis and B. subtilis 24 h later. The optimized co-culture parameters were as follows: total inoculation size, 24%; temperature, 32 °C; fermentation time, 6.5 days; and initial water content, 60%. The maximum TP yield was 28.37%. Notably, in the fermented MOLM (FMOLM), the content of nutrients such as crude protein (CP), small peptides, and total amino acids (AAs) were significantly increased relative to unfermented MOLM, whereas the contents of crude fiber (CF), tannin, and phytic acid were significantly decreased. MOLM analysis using scanning electron microscopy (SEM) revealed that SSF disrupted the surface structure of MOLM, and sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS-PAGE) indicated that macromolecular proteins were degraded. The in vitro protein digestibility (IVPD) of FMOLM was also improved significantly. Our findings suggest that multi-strain fermentation with A. niger, C. utilis and B. subtilis improves the nutritional quality of MOLM, rendering it a viable functional feedstuff for use in livestock industries in the future.

Purification of the phytase enzyme from Lactobacillus plantarum: The effect on pansy growth and macro-micro element content

In the present study, the phytase enzyme was purified from Lactobacillus plantarum with a 3.08% recovery, 9.57-purification fold, and with a specific activity of 278.82 EU/mg protein. Then, the effects of the 5 EU and 10 EU purified phytase was determined on the plant growth, quality, the macro-micro nutrient content of pansy (Viola × wittrockiana), which is of great importance in ornamental plants industry. The research was established under greenhouse conditions with natural light in 2017. The pansy seeds were coated with phytase enzyme solution, sown in a peat environment, and transferred to pots at the seedling period. In general, the 5 EU and 10 EU applications increase plant height, the number of leaves per plant, the number of side branches per plant, and flower height parameters compared to control. Also, micro- and macronutrient values in soil and plant samples were examined. According to the results, the phytase application on pansy cultivation positively affected the properties and yielded high quality of plants.

Fungal phytases: from genes to applications

Phytic acid stores 60-90% of the inorganic phosphorus in legumes, oil seeds, and cereals, making it inaccessible for metabolic processes in living systems. In addition, given its negative charge, phytic acid complexes with divalent cations, starch, and proteins. Inorganic phosphorous can be released from phytic acid upon the action of phytases. Phytases are phosphatases produced by animals, plants, and microorganisms, notably Aspergillus niger, and are employed as animal feed additive, in chemical industry and for ethanol production. Given the industrial relevance of phytases produced by filamentous fungi, this work discusses the functional characterization of fungal phytase-coding genes/proteins, highlighting the physicochemical parameters that govern the enzymatic activity, the development of phytase super-producing strains, and key features for industrial applications.

Genome-guided insights of tropical Bacillus strains efficient in maize growth promotion

Plant growth promoting bacteria (PGPB) are an efficient and sustainable alternative to mitigate biotic and abiotic stresses in maize. This work aimed to sequence the genome of two Bacillus strains (B116 and B119) and to evaluate their plant growth-promoting (PGP) potential in vitro and their capacity to trigger specific responses in different maize genotypes. Analysis of the genomic sequences revealed the presence of genes related to PGP activities. Both strains were able to produce biofilm and exopolysaccharides, and solubilize phosphate. The strain B119 produced higher amounts of IAA-like molecules and phytase, whereas B116 was capable to produce more acid phosphatase. Maize seedlings inoculated with either strains were submitted to polyethylene glycol-induced osmotic stress and showed an increase of thicker roots, which resulted in a higher root dry weight. The inoculation also increased the total dry weight and modified the root morphology of 16 out of 21 maize genotypes, indicating that the bacteria triggered specific responses depending on plant genotype background. Maize root remodeling was related to growth promotion mechanisms found in genomic prediction and confirmed by in vitro analysis. Overall, the genomic and phenotypic characterization brought new insights to the mechanisms of PGP in tropical Bacillus.

Partial characterization and purification of phytase from Lactobacillus plantarum CRL1964 isolated from pseudocereals

Cereals and pseudocereals are a rich source of nutrients and trace elements, but their dietary bioavailability is low due to the presence of phytate (IP6), an antinutritional compound with the ability to chelate cations and proteins. Phytase is an enzyme that catalyzes the hydrolysis of IP6 and it is used as an additive improving the nutritional quality of grain-based foods. The aim of this study was to select lactic acid bacteria (LAB) isolated from pseudocereals with phytase activity, characterize their production and activity, and purify the enzyme. LAB strains isolated from grains and spontaneous sourdough of quinoa and amaranth were grown in the Man Rogosa and Sharpe medium where the inorganic phosphate (Pi) was replaced by 1% of IP6. Phytase activity was determined by measuring the Pi released from IP6. Phytase of Lactobacillus (L.) plantarum CRL1964 (PhyLP) showed the highest specific activity from 73 LAB evaluated. IP6 induces PhyLP production, which is at its maximum at the end of the exponential phase. PhyLP was thermostable and maintained its activity under acidic conditions. The enzymatic activity is stimulated by ethylenediaminetetraacetic acid, Co²⁺, and ascorbic acid. PhyLP was partially purified and showed a molecular mass of 55 kDa. L. plantarum CRL1964 and/or PhyLP have the potential to be included in the processing of cereal/pseudocereals based products for animal feed and/or the food industry improving its nutritional value.

Prescience of endogenous regulation in Arabidopsis thaliana by Pseudomonas putida MTCC 5279 under phosphate starved salinity stress condition

Phosphorus (P) availability and salinity stress are two major constraints for agriculture productivity. A combination of salinity and P starvation is known to be more deleterious to plant health. Plant growth promoting rhizobacteria are known to ameliorate abiotic stress in plants by increasing the availability of different nutrients. However, interaction mechanisms of plant grown under salinity and P stress condition and effect of beneficial microbe for stress alleviation is still obscure. Earlier we reported the molecular insight of auxin producing, phosphate solubilising Pseudomonas putida MTCC 5279 (RAR) mediated plant growth promotion in Arabidopsis thaliana. In present study new trait of proline and phosphatase production of RAR and its impact on modulation of physiological phenomenon under phosphate starved-salinity stress condition in A. thaliana has been investigated. Different physiological and molecular determinants under RAR- A. thaliana interaction showed that auxin producing RAR shows tryptophan dependence for growth and proline production in ATP dependant manner under salinity stress. However, under P deprived conditions growth and proline production are independent of tryptophan. RAR mediated lateral root branching and root hair density through modulation of abscisic acid signalling was observed. Acidic phosphatase activity under P starved and salinity stress condition was majorly modulated along with ROS metabolism and expression of stress responsive/phosphate transporter genes. A strong correlation of different morpho-physiological factor with RAR + salt conditions, showed We concluded that enhanced adverse effect of salinity with unavailability of P was dampened in presence of P. putida MTCC 5279 (RAR) in A. thaliana, though more efficiently salinity stress conditions. Therefore, alleviation of combined stress of salinity induced phosphate nutrient deficiency by inoculation of beneficial microbe, P. putida MTCC 5279 offer good opportunities for enhancing the agricultural productivity.

Influence of Salt Stress on Growth of Spermosphere Bacterial Communities in Different Peanut (Arachis hypogaea L.) Cultivars

Background: Exposure of seeds to high salinity can cause reduced germination and poor seedling establishment. Improving the salt tolerance of peanut (Arachis hypogaea L.) seeds during germination is an important breeding goal of the peanut industry. Bacterial communities in the spermosphere soils may be of special importance to seed germination under salt stress, whereas extant results in oilseed crop peanut are scarce. Methods: Here, bacterial communities colonizing peanut seeds with salt stress were characterized using 16S rRNA gene sequencing. Results: Peanut spermosphere was composed of four dominant genera: Bacillus, Massilia, Pseudarthrobacter, and Sphingomonas. Comparisons of bacterial community structure revealed that the beneficial bacteria (Bacillus), which can produce specific phosphatases to sequentially mineralize organic phosphorus into inorganic phosphorus, occurred in relatively higher abundance in salt-treated spermosphere soils. Further soil enzyme activity assays showed that phosphatase activity increased in salt-treated spermosphere soils, which may be associated with the shift of Bacillus. Conclusion: This study will form the foundation for future improvement of salt tolerance of peanuts at the seed germination stage via modification of the soil microbes.

The pH Signaling Transcription Factor PAC-3 Regulates Metabolic and Developmental Processes in Pathogenic Fungi

The zinc finger transcription factor PAC-3/RIM101/PacC has a defined role in the secretion of enzymes and proteins in response to ambient pH, and also contributes to the virulence of species. Herein we evaluated the role of PAC-3 in the regulation of Neurospora crassa genes, in a model that examined the plant-fungi interactions. N. crassa is a model fungal species capable of exhibiting dynamic responses to its environment by employing endophytic or phytopathogenic behavior according to a given circumstance. Since plant growth and productivity are highly affected by pH and phosphorus (P) acquisition, we sought to verify the impact that induction of a Δpac-3 mutation would have under limited and sufficient Pi availability, while ensuring that the targeted physiological adjustments mimicked ambient pH and nutritional conditions required for efficient fungal growth and development. Our results suggest direct regulatory functions for PAC-3 in cell wall biosynthesis, homeostasis, oxidation-reduction processes, hydrolase activity, transmembrane transport, and modulation of genes associated with fungal virulence. Pi-dependent modulation was observed mainly in genes encoding for transporter proteins or related to cell wall development, thereby advancing the current understanding regarding colonization and adaptation processes in response to challenging environments. We have also provided comprehensive evidence that suggests a role for PAC-3 as a global regulator in plant pathogenic fungi, thus presenting results that have the potential to be applied to various types of microbes, with diverse survival mechanisms.

Toward a Regional Phosphorus (Re)cycle in the US Midwest

Redirecting anthropogenic waste phosphorus (P) flows from receiving water bodies to high P demand agricultural fields requires a resource management approach that integrates biogeochemistry, agronomy, engineering, and economics. In the US Midwest, agricultural reuse of P recovered from spatially colocated waste streams stands to reduce point-source P discharges, meet agricultural P needs, and-depending on the speciation of recovered P-mitigate P losses from agriculture. However, the speciation of P recovered from waste streams via its chemical transformation-referred to here as recovered P (rP) differs markedly based on waste stream composition and recovery method, which can further interact with soil and crop characteristics of agricultural sinks. The solubility of rP presents key tensions between engineered P recovery and agronomic reuse because it defines both the ability to remove organic and inorganic P from aqueous streams and the crop availability of rP. The potential of rP generation and composition differs greatly among animal, municipal, and grain milling waste streams due to the aqueous speciation of P and presence of coprecipitants. Two example rP forms, phytin and struvite, engage in distinct biogeochemical processes on addition to soils that ultimately influence crop uptake and potential losses of rP. These processes also influence the fate of nitrogen (N) embodied in rP. The economics of rP generation and reuse will determine if and which rP are produced. Matching rP species to appropriate agricultural systems is critical to develop sustainable and financially viable regional exchanges of rP from wastewater treatment to agricultural end users.

Genome Sequences of a Plant Beneficial Synthetic Bacterial Community Reveal Genetic Features for Successful Plant Colonization

Despite the availability of data on the functional and phylogenetic diversity of plant-associated microbiota, the molecular mechanisms governing the successful establishment of plant bacterial communities remain mostly elusive. To investigate bacterial traits associated with successful colonization of plants, we sequenced the genome of 26 bacteria of a synthetic microbial community (SynCom), 12 of which displayed robust and 14 displayed non-robust colonization lifestyles when inoculated in maize plants. We examined the colonization profile of individual bacteria in inoculated plants and inspected their genomes for traits correlated to the colonization lifestyle. Comparative genomic analysis between robust and non-robust bacteria revealed that commonly investigated plant growth-promoting features such as auxin production, nitrogen (N) fixation, phosphate acquisition, and ACC deaminase are not deterministic for robust colonization. Functions related to carbon (C) and N acquisition, including transporters of carbohydrates and amino acids, and kinases involved in signaling mechanisms associated with C and N uptake, were enriched in robust colonizers. While enrichment of carbohydrate transporters was linked to a wide range of metabolites, amino acid transporters were primarily related to the uptake of branched-chain amino acids. Our findings identify diversification of nutrient uptake phenotypes in bacteria as determinants for successful bacterial colonization of plants.

Regulatory rewiring through global gene regulations by PhoB and alarmone (p)ppGpp under various stress conditions

The phosphorus availability in soil ranged from <0.01 to 1 ppm and found limiting for the utilization by plants. Hence, phosphate solubilizing bacteria (PSB) proficiently fulfill the phosphorus requirement of plants in an eco-friendly manner. The PSB encounter dynamic and challenging environmental conditions viz., high temperature, osmotic, acid, and climatic changes often hamper their activity and proficiency. The modern trend is shifting from isolation of the PSB to their genetic potentials and genome annotation not only for their better performance in the field trials but also to study their ability to cope up with stresses. In order to withstand environmental stress, bacteria need to restructure its metabolic network to ensure its survival. Pi starving condition response regulator (PhoB) and the mediator of stringent stress response alarmone (p)ppGpp known to regulate the global regulatory network of bacteria to provide balanced physiology under various stress condition. The current review discusses the global regulation and crosstalk of genes involved in phosphorus homeostasis, solubilization, and various stress response to fine tune the bacterial physiology. The knowledge of these network crosstalk help bacteria to respond efficiently to the challenging environmental parameters, and their physiological plasticity lead us to develop proficient long-lasting consortia for plant growth promotion.

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.

Use of plant growth promoting Rhizobacteria (PGPR) and mycorrhizae to improve the growth and nutrient utilization of common bean in a soil infected with white rot fungi

Extensive use of fertilizers and pesticides led to dangerous ecological effects and therefore the biological approaches have been widely recommended to prevent further deterioration for the environment. The current study was conducted to explore the potentiality of using single or combined inoculations by mycorrhizae, Bacillus subtilis and Pseudomonas fluorescence for controlling the infection of common bean plants with Sclerotium rolfsii on one hand and as bio-fertilizers for improving plants nutritional status on the other hand. The soil of study was mildly infected with S. rolfsii and contained high total-P content. Thus, minimal P inputs were added to the inoculated soil in the form of rock phosphate. Activities of plant defense enzymes i.e. chitinase, peroxidase and polyphenol oxidase were determined under the greenhouse conditions and the results obtained herein indicated that activities of such enzymes increased significantly owing to bio-agent inoculations. In this concern, combined treatments resulted in further significant increases over the single ones. A field study was then conducted for two successive years and the results reveal that single inoculations increased straw and green pod yields as well as the uptake of P and Fe by plants as compared with the non-inoculated treatment. Combined inoculants recorded further significant increases in these parameters even when compared with the fungicide treated plants. Generally, straw and pod yields obtained from the second growing season were significantly higher than those attained in the first growing one. Our study confirms the success of the used bio-treatments in minimizing soil pollution through fertilizer and/or pesticide inputs.

Abiotic phosphorus recycling from adsorbed ribonucleotides on a ferrihydrite-type mineral: Probing solution and surface species

Iron (Fe) (oxyhydr)oxide minerals, which are amongst most reactive minerals in soils and sediments, are known to exhibit strong adsorption of inorganic phosphate (P_i) and organophosphate (P_o) compounds. Beyond synthetic P_o compounds, much still remains unknown about the reactivity of these minerals to transform naturally-occurring P_o compounds to P_i, particularly with respect to solution versus surface speciation of P_o hydrolysis. To investigate this reactivity with a ferrihydrite-type mineral and ribonucleotides, we employed high-resolution liquid chromatography-mass spectrometry (LC-MS), X-ray absorption near-edge structure (XANES), Fourier-transform infrared (FTIR) spectroscopy, and molecular modeling. Kinetic experiments were conducted with the mineral (1 g L^-1) reacted with adenosine monophosphate, diphosphate, or triphosphate (respectively AMP, ADP, ATP; 50 µM). Analysis of solution organic species by LC-MS implied that only adsorption occurred with AMP and ADP but both adsorption and dephosphorylation of ATP were evident. Maximum adsorption capacities per gram of mineral were 40.6 ± 0.8 µmol AMP, 35.7 ± 1.6 µmol ADP, and 10.9 ± 1.0 µmol ATP; solution dephosphorylated by-products accounted for 15% of initial ATP. Subsequent XANES analysis of the surface species revealed that 16% of adsorbed AMP and 30% of adsorbed ATP were subjected to dephosphorylation, which was not fully quantifiable from the solution measurements. Molecular simulations predicted that ADP and ATP were complexed mainly via the phosphate groups whereas AMP binding also involved multiple hydrogen bonds with the adenosine moiety; our FTIR data confirmed these binding confirmations. Our findings thus imply that specific adsorption mechanisms dictate the recycling and subsequent trapping of P_i from ribonucleotide-like biomolecules reacted with Fe (oxyhydr)oxide minerals.

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.

Syntrophic effect of indigenous and inoculated microorganisms in the leaching of rare earth elements from Western Australian monazite

The unique physiochemical properties exhibited by rare earth elements (REEs) and their increasing application in high-tech industries has created a demand for secure supply lines with established recovery procedures that create minimal environmental damage. Bioleaching experiments conducted on a non-sterile monazite concentrate with a known phosphate solubilising microorganism (PSM) resulted in greater mobilisation of REEs into solution in comparison to experiments conducted on sterile monazite. By combining the native consortia with an introduced PSM, a syntrophic effect between the populations effectively leached a greater amount of REEs than either a single PSM or the indigenous population alone. With sterile monazite, Penicillium sp.CF1 inoculated experiments released a total REE concentration of 12.32 mg L^-1 after incubation for 8 days, whereas on non-sterile ore, double the soluble REE concentration was recorded (23.7 mg L^-1). Comparable effects were recorded with Enterobacter aerogenes, Pantoea agglomerans and Pseudomonas putida. Alterations in the microbial populations during bioleaching of the monazite ore were determined by diversity profiling and demonstrated noticeable changes in community inhabitants over 14 days. The presence of native Firmicutes on the monazite appears to greatly contribute to the increased leaching recorded when using non-sterile monazite for REE recovery.

Analysis of Microbial Functions in the Rhizosphere Using a Metabolic-Network Based Framework for Metagenomics Interpretation

Advances in metagenomics enable high resolution description of complex bacterial communities in their natural environments. Consequently, conceptual approaches for community level functional analysis are in high need. Here, we introduce a framework for a metagenomics-based analysis of community functions. Environment-specific gene catalogs, derived from metagenomes, are processed into metabolic-network representation. By applying established ecological conventions, network-edges (metabolic functions) are assigned with taxonomic annotations according to the dominance level of specific groups. Once a function-taxonomy link is established, prediction of the impact of dominant taxa on the overall community performances is assessed by simulating removal or addition of edges (taxa associated functions). This approach is demonstrated on metagenomic data describing the microbial communities from the root environment of two crop plants – wheat and cucumber. Predictions for environment-dependent effects revealed differences between treatments (root vs. soil), corresponding to documented observations. Metabolism of specific plant exudates (e.g., organic acids, flavonoids) was linked with distinct taxonomic groups in simulated root, but not soil, environments. These dependencies point to the impact of these metabolite families as determinants of community structure. Simulations of the activity of pairwise combinations of taxonomic groups (order level) predicted the possible production of complementary metabolites. Complementation profiles allow formulating a possible metabolic role for observed co-occurrence patterns. For example, production of tryptophan-associated metabolites through complementary interactions is unique to the tryptophan-deficient cucumber root environment. Our approach enables formulation of testable predictions for species contribution to community activity and exploration of the functional outcome of structural shifts in complex bacterial communities. Understanding community-level metabolism is an essential step toward the manipulation and optimization of microbial function. Here, we introduce an analysis framework addressing three key challenges of such data: producing quantified links between taxonomy and function; contextualizing discrete functions into communal networks; and simulating environmental impact on community performances. New technologies will soon provide a high-coverage description of biotic and a-biotic aspects of complex microbial communities such as these found in gut and soil. This framework was designed to allow the integration of high-throughput metabolomic and metagenomic data toward tackling the intricate associations between community structure, community function, and metabolic inputs.

Let the Core Microbiota Be Functional

The microbial community that is systematically associated with a given host plant is called the core microbiota. The definition of the core microbiota was so far based on its taxonomic composition, but we argue that it should also be based on its functions. This so-called functional core microbiota encompasses microbial vehicles carrying replicators (genes) with essential functions for holobiont (i.e., plant plus microbiota) fitness. It builds up from enhanced horizontal transfers of replicators as well as from ecological enrichment of their vehicles. The transmission pathways of this functional core microbiota vary over plant generations according to environmental constraints and its added value for holobiont fitness.

Genetically modified phytase crops role in sustainable plant and animal nutrition and ecological development: a review

Globally, plant-derivatives especially cereals and legumes are the major staple food sources for animals. The seeds of these crops comprise of phytic acid, the major repository form of the phosphorus, which is not digestible by simple-stomached animals. However, it is the most important factor responsible for impeding the absorption of minerals by plants that eventually results in less use of fertilizers that ultimately cause eutrophication in water bodies. Although abundant phosphorus (P) exists in the soils, plants cannot absorb most of the P due to its conversion to unavailable forms. Hence, additional P supplementation is indispensable to the soil to promote crop yields which not only leads to soil infertility but also rapid depletion of non-renewable P reservoirs. Phytase/phosphatase enzyme is essential to liberate P from soils by plants and from seeds by monogastric animals. Phytases are kind of phosphatases which can hydrolyse the indigestible phytate into inorganic Phosphate (Pi) and lower myo-inositol. There are several approaches to mitigate the problems associated with phytate indigestibility. One of the best possible solutions is engineering crops to produce heterologous phytase to improve P utilization by monogastric animals, plant nutrition and sustainable ecological developments. Previously published reviews were focused on either soil phytate or seed-phytate, related issues, but this review will address both the problems as well as phytate related ecological problems. This review summarizes the overall view of engineered phytase crops and their role in sustainable agriculture, animal nutrition and ecological development.