From Isolation of Phosphate Solubilizing Microbes to Their Formulation and Use as Biofertilizers: Status and Needs

Studies on the Phosphorus-Solubilizing Ability of Isaria cateinannulata and Its Influence on the Growth of Fagopyrum tataricum Plants

I. cateinannulata has been shown to promote the growth of F. tataricum. However, whether its growth-promoting capacity is related to its ability to solubilize phosphorus has not been reported. Therefore, in this study, we sought to assess the phosphorus-solubilizing ability of 18 strains of I. cateinannulata by analyzing their growth in an inorganic phosphorus culture medium. The effects of F. tataricum on growth and effective phosphorus content were analyzed through field experiments. The results showed that all 18 strains of I. cateinannulata had a phosphorus release capacity, with phosphorus solubilization ranging from 5.14 ± 0.37 mg/L to 6.21 ± 0.01 mg/L, and strain 9 exhibited the best phosphorus solubilization effect. Additionally, the field results demonstrated that I. cateinannulata positively influenced the growth, root length, and yield of F. tataricum by increasing the chlorophyll and soluble phosphorus content. This study will provide a material basis and theoretical support for investigating the interaction mechanism between I. cateinannulata and F. tataricum.

Food waste-based bio-fertilizers production by bio-based fermenters and their potential impact on the environment

Increasing food waste is creating a global waste (and management) crisis. Globally, ∼1.6 billion tons of food is wasted annually, worth ∼$1.2 trillion. By reducing this waste or by turning it into valuable products, numerous economic advantages can be realized, including improved food security, lower production costs, biodegradable products, environmental sustainability, and cleaner solutions to the growing world's waste and garbage management. The appropriate handling of these detrimental materials can significantly reduce the risks to human health. Food waste is available in biodegradable forms and, with the potential to speed up microbial metabolism effectively, has immense potential in improving bio-based fertilizer generation. Synthetic inorganic fertilizers severely affect human health, the environment, and soil fertility, thus requiring immediate consideration. To address these problems, agricultural farming is moving towards manufacturing bio-based fertilizers via utilizing natural bioresources. Food waste-based bio-fertilizers could help increase yields, nutrients, and organic matter and mitigate synthetic fertilizers' adverse effects. These are presented and discussed in the review.

Genomics analysis of three phosphorus-dissolving bacteria isolated from Torreya grandis soil

With the increasingly serious problem of phosphorus deficiency in the subtropical zone, chemical fertilizers are widely used. But it pollutes the environment. Phosphorus-solubilizing microorganisms (PSMs) are referred to as a new solution to this problem. We explored the phosphorus-dissolving characteristics of PSB strains isolated from the rhizosphere soil of Torreya grandis to provide a theoretical basis for selecting the strain for managing phosphorus deficiency in subtropical soils and also provides a more sufficient theoretical basis for the utilization of PSMs. From 84 strains, three strains exhibiting high phosphorus solubility and strong IAA producing capacity were selected through a series of experiments. The phosphate-solubilizing capacity of the three selected strains W1, W74, and W83 were 339.78 mg/L, 332.57 mg/L, and 358.61 mg/L, respectively. Furthermore, W1 showed the strongest IAA secreting capacity of 8.62 mg/L, followed by W74 (7.58 mg/L), and W83 (7.59 mg/L). Determination by metabolites, it was observed that these three strains dissolved phosphorus by secreting a large amount of lactic acid, aromatic acid, and succinic acid. The genome of these PSBs were sequenced and annotated in this study. Our results revealed that PSB primarily promotes their metabolic pathway, especially carbon metabolism, to secrete plenty organic acids for dissolving insoluble phosphorus.

A study of microbial diversity in a biofertilizer consortium

Biofertilizers supply living microorganisms to help plants grow and keep their health. This study examines the microbiome composition of a commercial biofertilizer known for its plant growth-promoting activity. Using ITS and 16S rRNA gene sequence analyses, we describe the microbial communities of a biofertilizer, with 163 fungal species and 485 bacterial genera found. The biofertilizer contains a variety of microorganisms previously reported to enhance nutrient uptake, phytohormone production, stress tolerance, and pathogen resistance in plants. Plant roots created a microenvironment that boosted bacterial diversity but filtered fungal communities. Notably, preserving the fungal-inoculated substrate proves critical for keeping fungal diversity in the root fraction. We described that bacteria were more diverse in the rhizosphere than in the substrate. In contrast, root-associated fungi were less diverse than the substrate ones. We propose using plant roots as bioreactors to sustain dynamic environments that promote the proliferation of microorganisms with biofertilizer potential. The study suggests that bacteria grow close to plant roots, while root-associated fungi may be a subset of the substrate fungi. These findings show that the composition of the biofertilizer may be influenced by the selection of microorganisms associated with plant roots, which could have implications for the effectiveness of the biofertilizer in promoting plant growth. In conclusion, our study sheds light on the intricate interplay between plant roots and the biofertilizer's microbial communities. Understanding this relationship can aid in optimizing biofertilizer production and application, contributing to sustainable agricultural practices and improved crop yields.

Modification of pectin/starch-based beads with additives to improve Bacillus subtilis encapsulation for agricultural applications

The use of Bacillus as biofertilizer is a sustainable strategy to increase agricultural productivity, but it still requires the development of formulations to protect cells from stressful conditions. Ionotropic gelation using a pectin/starch matrix is a promising encapsulation strategy to achieve this goal. By incorporating additives such as montmorillonite (MMT), attapulgite (ATP), polyethylene glycol (PEG), and carboxymethyl cellulose (CMC), the properties of these encapsulated products could be further improved. In this study, we investigated the influence of these additives on the properties of pectin/starch-based beads for the encapsulation of Bacillus subtilis. FTIR analysis indicated pectin and Ca2+ ions interactions, while the XRD showed good dispersion of clays in the materials. SEM and X-ray microtomography revealed differences in the morphology of the beads due to the use of the additives. The viabilities at the encapsulation were higher than 1010 CFU g-1 for all formulations, with differences in the release profiles. In terms of cell protection, the pectin/starch, pectin/starch-MMT and pectin/starch-CMC formulations showed the highest cell viability after exposure to fungicide, while the pectin/starch-ATP beads showed the best performance after UV exposure. Moreover, all formulations maintained more than 109 CFU g-1 after six months of storage, which meets values required for microbial inoculants.

Improving the efficiency of phosphate rocks combined with phosphate solubilizing Actinomycetota to increase wheat growth under alkaline and acidic soils

Low availability of phosphorus (P) in both acidic and alkaline soils is a major problem for sustainable improvement in wheat crops yield. Optimization of crops productivity can be achieved by increasing the bioavailability of P by phosphate solubilizing Actinomycetota (PSA). However, their effectiveness may vary with changing agro-climatic conditions. In this regard, a greenhouse experiment was conducted to assess the interaction inoculation of five potential PSA (P16-P18-BC3-BC10 and BC11) and RPs (RP1- RP2-RP3 and RP4) on the growth and yield of wheat crop in unsterilized P- deficient alkaline and acidic soils. Their performance was compared with single super phosphate (TSP) and reactive RP (BG4). The in-vitro tests showed that all PSA colonize wheat root and form a strong biofilm except Streptomyces anulatus strain P16. Our findings revealed that all PSA significantly improve the shoot/root dry weights, spike biomass, chlorophyll contents as well as nutrients uptake in plants fertilized with RP3 and RP4. However, the combined application of Nocardiopsis alba BC11 along with RP4 in alkaline soil, was effective in optimizing wheat yield attributes and improve the yield biomass up to 19.7% as compared to the triple superphosphate (TSP). This study supports the view that the inoculation with Nocardiopsis alba BC11 has a broad RP solubilization and could alleviate the agricultural losses due to P limitation in acidic and alkaline soils.

Biotic and abiotic effects of soil organic matter on the phytoavailable phosphorus in soils: a review

Soil organic matter (SOM) has a critical role in regulating soil phosphorus (P) dynamics and producing phytoavailable P. However, soil P dynamics are often explained mainly by the effects of soil pH, clay contents, and elemental compositions, such as calcium, iron, and aluminum. Therefore, a better understanding of the mechanisms of how SOM influences phytoavailable P in soils is required for establishing effective agricultural management for soil health and enhancement of soil fertility, especially P-use efficiency. In this review, the following abiotic and biotic mechanisms are discussed; (1) competitive sorption between SOM with P for positively charged adsorption sites of clays and metal oxides (abiotic reaction), (2) competitive complexations between SOM with P for cations (abiotic reaction), (3) competitive complexations between incorporation of P by binary complexations of SOM and bridging cations with the formation of stable P minerals (abiotic reaction), (4) enhanced activities of enzymes, which affects soil P dynamics (biotic reaction), (5) mineralization/immobilization of P during the decay of SOM (biotic reaction), and (6) solubilization of inorganic P mediated by organic acids released by microbes (biotic reaction).

Regeneration of cocoa (Theobroma cacao L.) via somatic embryogenesis: Key aspects in the in vitro conversion stage and in the ex vitro adaptation of plantlets

Adapting plantlets to ex vitro conditions is a decisive step in the micropropagation process via organogenesis or somatic embryogenesis (ES). The percentage of success in this stage determines the quality of the product, an example of which is found in cocoa plantlets regenerated by ES, which require specific conditions to overcome the stress of the new environment. Considering the quality of the in vitro plantlets largely determines the survival and growth in ex vitro conditions, the effect of two culture media between the embryo maturation stage and the initial stage of conversion to plantlet was evaluated (EM2 - MM6 and EM2 – MF medium), achieving with the latter greater stem height, root length and the number of true leaves. In the final stage of the conversion and growth of the plantlet, the effect of five culture media was evaluated (ENR6, MF, ENR8, EDL, PR), achieving better results in stem height, root length, and the number of true leaves on MF medium. In addition, it was found that the transition of the EM2-MF had a significant development in the presence of the desired pivoting root and fibrous roots. Under nursery conditions, the growth and development of the plantlets was tested through the inoculation of beneficial microorganisms to promote survival. The plantlets that met the minimum morphological parameters for acclimation were planted in a substrate of coconut palm and sand (3:1 v/v) previously selected in the laboratory (BS). The effect of Pseudomonas ACC deaminase (PAACd), Trichoderma asperellum (Ta) and arbuscular mycorrhiza forming fungus (AMF) and different concentrations of phosphorus (PC) (0%, 50% and 100%) in the Hoagland nutrient solution (1:10) was evaluated. First, for CCN5, 62.5% of survival was obtained with PAACd + AMF. Second, the largest leaf size and survival were obtained with PAACd + Ta for CNCh12 and CCN51; likewise, for CNCh13, the best result was obtained with PAACd. Keywords: Cacao, Clonal propagation, Mycorrhiza, Pseudomonas, Trichoderma.

The mechanism of phosphate solubilizing of Pseudomonas sp. TC952 and its solubilizing process on TC removal

Antibiotics undergo a series of complex transport and transformation route after entering the environment; however, there is scarce information about the effects of the bacterial phosphate-solubilizing process on tetracycline (TC) transformation. In this study, Pseudomonas sp. TC952 was identified as phosphate-solubilizing bacterium with high phosphate-solubilizing ability even under TC stress; it could solubilize maximum phosphate with a production of 400 mg/L soluble phosphate in 2 days. TC did not affect phosphate solubilizing in a short time incubation, but slightly promoted in a long incubation time. TC was adsorbed by inorganic phosphate with high efficiency of 53.09% within 1 day. Four tetracycline antibiotic resistance and sixteen inorganic phosphate-solubilizing-related genes were identified in the genome, which revealed the phosphate-solubilizing mechanism was that strain TC952 secrete organic acid to resolve inorganic phosphate and also secrete siderophore to chelate inorganic phosphate. So, during the inorganic phosphate-solubilizing process of strain TC952, TC was de-adsorbed from inorganic phosphate, and the solution was acidified into pH 4.3 through secreting organic acid to dissolve inorganic phosphorus, which resulted in Ca²⁺ and PO₄^3- releasing into the solution. Finally, the acidic condition and PO₄^3- enhanced TC hydrolysis. The mechanism of phosphate-solubilizing process on TC removal and genome analysis provides us new insight of the TC migration and transformation route in the environment.

Integrated analysis of potential microbial consortia, soil nutritional status, and agro-climatic datasets to modulate P nutrient uptake and yield effectiveness of wheat under climate change resilience

Climate change has a devastating effect on wheat production; therefore, crop production might decline by 2030. Phosphorus (P) nutrient deficiency is another main limiting factor of reduced yield. Hence, there is a dire need to judiciously consider wheat yield, so that human requirements and nutrition balance can be sustained efficiently. Despite the great significance of biostimulants in sustainable agriculture, there is still a lack of integrated technology encompassing the successful competitiveness of inoculated phosphate-solubilizing bacteria (PSB) in agricultural systems in the context of climatic conditions/meteorological factors and soil nutritional status. Therefore, the present study reveals the modulation of an integrated P nutrient management approach to develop potential PSB consortia for recommended wheat varieties by considering the respective soil health and agro-climatic conditions. The designed consortia were found to maintain adequate viability for up to 9 months, verified through field emission scanning electron microscopy and viable count. Furthermore, a significant increase in grain yield (5%-8%) and seed P (4%) content was observed in consortia-inoculated wheat plants with 20% reduced Diammonium phosphate (DAP) application under net house conditions. Fluorescence in situ hybridization analysis of roots and amplification of the gcd gene of Ochrobactrum sp. SSR indicated the survival and rhizosphere competency of the inoculated PSB. Categorical principal component analysis (CAT-PCA) showed a positive correlation of inoculated field-grown wheat varieties in native soils to grain yield, soil P content, and precipitation for sites belonging to irrigated plains and seed P content, soil organic matter, and number of tillers for sites belonging to Northern dry mountains. However, the impact of inoculation at sites belonging to the Indus delta was found significantly correlated to soil potassium (K) content, electrical conductivity (EC), and temperature. Additionally, a significant increase in grain yield (15%) and seed P (14%) content was observed in inoculated wheat plants. Thus, the present study demonstrates for the first time the need to integrate soil biological health and agro-climatic conditions for consistent performance of augmented PSB and enhanced P nutrient uptake to curtail soil pollution caused by the extensive use of agrochemicals. This study provides innovative insights and identifies key questions for future research on PSB to promote its successful implementation in agriculture.

SCAR marker: A potential tool for authentication of agriculturally important microorganisms

Microbial inoculants are globally recommended for plant growth promotion and control of plant pathogens. These inoculants require stringent quality checks for sustainable field efficacy. Questionable regulatory frameworks constantly deteriorate the reliability of bio-inoculant technology. Existing global regulations do not involve any rapid molecular technique for the routine inspection of microbial preparations. Sequence characterized amplified region (SCAR) marker offers rapid and precise strain-level authentication of target microbes. Such advanced molecular techniques must be exploited to accurately validate the microbial formulations. Besides, the global dissemination of plant pathogenic microbes has always been an alarming threat to food security. SCAR markers could be used at the plant quarantine centers to rapidly detect catastrophic pathogens, thereby circumventing the import and export of contagious plant materials. The current review is focused on promoting the SCAR marker technology to validate commercial bio-inoculants and predict plant pandemics.

A study of potent biofertiliser and its degradation ability of monocrotophos and its in silico analysis

Potassium (K) and phosphorus (P) are the important macronutrients needed for the plant development, but it is widely present in an insoluble form for the plant's uptake. In order to increase the productivity, biofertilisers play crucial role in plant growth enhancement. Our present work focused to isolate potassium-phosphate solubilizing bacteria from the agricultural soil of tomato cultivated soil. Potassium and phosphate solubilization and degradation of monocrotophos was estimated spectrophotometrically. Out of thirteen isolates, two isolates proved to be the best P and K solubilizers. The bacterial isolates (SDKVG02 and SDKVG04) were optimized to obtain maximum P and K solubilization of 57.5 mg L-1 and 15.07 mg L-1 by the isolates. Pot experiments were conducted using SDKVG 02 and 04, immobilized on carrier materials, peat proving the best carrier with the total average green gram and chick pea length of 11.66 ± 0.0666 22.22 ± 0.0577. The MCP degradation percentage was achieved at 80 ppm of MCP with 75.8% and 64.10% by SDKVG 02 and SDKVG 04. Furthermore, production of organic acids such as malic acid, phthalic acid, ascorbic acid, nicotinic acid, and tartaric acid paves solubilization of P and K. The isolates were recognized based on 16S rRNA gene sequencing as Enterobacter hormaechei- SDKVG-02, Enterobacter cloacae SDKVG- 04. The KSB-PSB isolates also express N-fixing activity which is proved through In-silico analysis. It is worth to highlight SDKVG 02 and 04 would be potent biofertiliser exploited in increasing the soil fertility and crop productivity as well in degradation of monocrotophos present in the soil.

Plant growth-promoting properties of the phosphate-solubilizing red yeast Rhodosporidium paludigenum

Phosphorus (P) is one of the essential elements that are necessary for plant development and growth. However, the availability of soluble forms of P for plants in the soils is limited, because a large proportion of it is bound to soil constituents. Thus, the concentration of P available to plants at any time is very low and, moreover, its availability depends on the soil pH. As a solution, phosphate-solubilizing microorganisms (PSMs) are employed that render inorganic P available to plants in soluble form. Thus far, research into PSMs has been insufficient, and only few such organisms have been considered for exploitation as microbial fertilizer strains. The characteristics of plant growth promotion with the plant-PSMs coculture system remain to be elucidated. In the current study, we report on the isolate Rhodosporidium paludigenum JYC100 that exhibits good performance for solubilizing calcium phosphate. We found that it can be regulated by the amount of soluble phosphate. Furthermore, R. paludigenum JYC100 promotes plant growth under specific conditions (P deficiency, but with insoluble phosphate) in different media and soil pots. In contrast, the yeast Aureobasidium pullulans JYC104 exhibited weak phosphate-solubilizing capacities and no plant growth-promoting ability. Compared to control plants, the biomass, shoot height, and cellular inorganic P content of plants increased in plants cocultivated with R. paludigenum JYC100. In addition, histochemical GUS and qRT-PCR assays of phosphate starvation-induced (PSI) genes showed that the transcript levels of these PSI genes are decreased in the plants cocultured with R. paludigenum JYC100. These findings reflect the unique ability of R. paludigenum JYC100 to convert insoluble P compounds to plant-available P, thereby leading to growth promotion. Our study results highlight the use of yeasts as potential substitutes for inorganic phosphate fertilizers to meet the P demands of plants, which may eventually improve yields in sustainable agricultures.

Diversity, mechanisms and beneficial features of phosphate-solubilizing Streptomyces in sustainable agriculture: A review

Currently, the use of phosphate (P) biofertilizers among many bioformulations has attracted a large amount of interest for sustainable agriculture. By acting as growth promoters, members of the Streptomyces genus can positively interact with plants. Several studies have shown the great potential of this bacterial group in supplementing P in a soluble, plant-available form by several mechanisms. Furthermore, some P-solubilizing Streptomyces (PSS) species are known as plant growth-promoting rhizobacteria that are able to promote plant growth through other means, such as increasing the availability of soil nutrients and producing a wide range of antibiotics, phytohormones, bioactive compounds, and secondary metabolites other than antimicrobial compounds. Therefore, the use of PSS with multiple plant growth-promoting activities as an alternative strategy appears to limit the negative impacts of chemical fertilizers in agricultural practices on environmental and human health, and the potential effects of these PSS on enhancing plant fitness and crop yields have been explored. However, compared with studies on the use of other gram-positive bacteria, studies on the use of Streptomyces as P solubilizers are still lacking, and their results are unclear. Although PSS have been reported as potential bioinoculants in both greenhouse and field experiments, no PSS-based biofertilizers have been commercialized to date. In this regard, this review provides an overview mainly of the P solubilization activity of Streptomyces species, including their use as P biofertilizers in competitive agronomic practices and the mechanisms through which they release P by solubilization/mineralization, for both increasing P use efficiency in the soil and plant growth. This review further highlights and discusses the beneficial association of PSS with plants in detail with the latest developments and research to expand the knowledge concerning the use of PSS as P biofertilizers for field applications by exploiting their numerous advantages in improving crop production to meet global food demands.

Differential colonization and functioning of microbial community in response to phosphate levels

Microbes play a major role in phosphate cycling and regulate its availability in various environments. The metagenomic study highlights the microbial community divergence and interplay of phosphate metabolism functional genes in response to phosphate rich (100 mgL^-1), limiting (25 mgL^-1), and stressed (5 mgL^-1) conditions at lab-scale bioreactor. Total five core phyla were found responsive toward different phosphate (Pi) levels. However, major variations were observed in Proteobacteria and Actinobacteria with 33-81% and 5-56% relative abundance, respectively. Canonical correspondence analysis reflects the colonization of Sinorhizobium (0.8-4%), Mesorhizobium (1-4%), Rhizobium (0.5-3%) in rich condition whereas, Pseudomonas (1-2%), Rhodococcus (0.2-2%), Flavobacterium (0.2-1%) and Streptomyces (0.3-4%) colonized in limiting and stress condition. The functional profiling demonstrates that Pi limiting and stress condition subjected biomass were characterized by abundant PQQ-Glucose dehydrogenase, alkaline phosphatase, 5'-nucleotidase, and phospholipases C genes. The finding implies that the major abundant genera belonging to phosphate solubilization enriched in limiting/stressed conditions decide the functional turnover by modulating the metabolic flexibility for Pi cycling. The study gives a better insight into intrinsic ecological responsiveness mediated by microbial communities in different Pi conditions that would help to design the microbiome according to the soil phosphate condition. Furthermore, this information assists in sustainably maintaining the ecological balance by omitting excessive chemical fertilizers and eutrophication.

Plant growth-promoting rhizobacterial biofertilizers for crop production: The past, present, and future

Recent decades have witnessed increased agricultural production to match the global demand for food fueled by population increase. Conventional agricultural practices are heavily reliant on artificial fertilizers that have numerous human and environmental health effects. Cognizant of this, sustainability researchers and environmentalists have increased their focus on other crop fertilization mechanisms. Biofertilizers are microbial formulations constituted of indigenous plant growth-promoting rhizobacteria (PGPR) that directly or indirectly promote plant growth through the solubilization of soil nutrients, and the production of plant growth-stimulating hormones and iron-sequestering metabolites called siderophores. Biofertilizers have continually been studied, recommended, and even successfully adopted for the production of many crops in the world. These microbial products hold massive potential as sustainable crop production tools, especially in the wake of climate change that is partly fueled by artificial fertilizers. Despite the growing interest in the technology, its full potential has not yet been achieved and utilization still seems to be in infancy. There is a need to shed light on the past, current, and future prospects of biofertilizers to increase their understanding and utility. This review evaluates the history of PGPR biofertilizers, assesses their present utilization, and critically advocates their future in sustainable crop production. It, therefore, updates our understanding of the evolution of PGPR biofertilizers in crop production. Such information can facilitate the evaluation of their potential and ultimately pave the way for increased exploitation.

Streptomycetaceae and Promicromonosporaceae: Two Actinomycetes Families from Moroccan Oat Soils Enhancing Solubilization of Natural Phosphate

Soil actinomycetes explorations appear to be an efficient alternative as biofertilizers to optimize the use of phosphorus (P) resources and enhance plant growth. This research aimed to explore the distribution of actinomycetes isolated from four different rhizospheric Moroccan oat soils and to investigate their potential for P solubilization. The distribution of actinomycetes was significantly more abundant in Settat (9.68%), Tangier (7.38%), and Beni Mellal (6.87%) than in the Merchouch-Rabat (4.90%) region. A total of 235 actinomycete strains were isolated from all sites and tested for their ability to grow on a synthetic minimum medium (SMM) containing insoluble natural rock phosphate (RP) or synthetic tricalcium phosphate (TCP) as the unique P source. One hundred forty-three isolates (60.8%) had the ability to grow in the SMM with RP whereas only twenty-five isolates (17%) had the most active growth using the SMM with TCP. Eight isolates with the most active growth in solid SMM were selected for their P solubilization abilities in liquid SMM cultures. The highest amount of P solubilized was 163.8 µg/mL for RP and 110.27 µg/mL for TCP after 5 days of culture. The biosolubilization process of AM2, the most efficient RP and TCP solubilizing strain, probably implied the highest excretion of siderophore substances. Eight of these strains were shown to belong to the Streptomyces genus and one to the Promicromonospora genus. These findings bolster the phosphate biosolubilization abilities of actinomycetes and may participate in increasing agricultural yields in an eco-efficient and environmentally friendly manner.

Climate-Resilient Microbial Biotechnology: A Perspective on Sustainable Agriculture

We designed this review to describe a compilation of studies to enlighten the concepts of plant–microbe interactions, adopted protocols in smart crop farming, and biodiversity to reaffirm sustainable agriculture. The ever-increasing use of agrochemicals to boost crop production has created health hazards to humans and the environment. Microbes can bring up the hidden strength of plants, augmenting disease resistance and yield, hereafter, crops could be grown without chemicals by harnessing microbes that live in/on plants and soil. This review summarizes an understanding of the functions and importance of indigenous microbial communities; host–microbial and microbial–microbial interactions; simplified experimentally controlled synthetic flora used to perform targeted operations; maintaining the molecular mechanisms; and microbial agent application technology. It also analyzes existing problems and forecasts prospects. The real advancement of microbiome engineering requires a large number of cycles to obtain the necessary ecological principles, precise manipulation of the microbiome, and predictable results. To advance this approach, interdisciplinary collaboration in the areas of experimentation, computation, automation, and applications is required. The road to microbiome engineering seems to be long; however, research and biotechnology provide a promising approach for proceeding with microbial engineering and address persistent social and environmental issues.

The Effects of Plant Health Status on the Community Structure and Metabolic Pathways of Rhizosphere Microbial Communities Associated with Solanum lycopersicum

Powdery mildew disease caused by Oidium neolycopersici is one of the major diseases affecting tomato production in South Africa. Interestingly, limited studies exist on how this disease affects the community structure microbial communities associated with tomato plants employing shotgun metagenomics. In this study, we assess how the health status of a tomato plant affects the diversity of the rhizosphere microbial community. We collected soil samples from the rhizosphere of healthy (HR) and diseased (DR; powdery mildew infected) tomatoes, alongside bulk soil (BR), extracted DNA, and did sequencing using shotgun metagenomics. Our results demonstrated that the rhizosphere microbiome alongside some specific functions were abundant in HR followed by DR and bulk soil (BR) in the order HR > DR > BR. We found eighteen (18) bacterial phyla abundant in HR, including Actinobacteria, Acidobacteria, Aquificae, Bacteroidetes, etc. The dominant fungal phyla include; Ascomycota and Basidiomycota, while the prominent archaeal phyla are Thaumarchaeota, Crenarchaeota, and Euryarchaeota. Three (3) bacteria phyla dominated the DR samples; Bacteroidetes, Gemmatimonadetes, and Thermotoga. Our result also employed the SEED subsystem and revealed that the metabolic pathways involved were abundant in HR. The α-diversity demonstrates that there is no significant difference among the rhizosphere microbiomes across the sites, while β-diversity demonstrated a significant difference.

Designing Synergistic Biostimulants Formulation Containing Autochthonous Phosphate-Solubilizing Bacteria for Sustainable Wheat Production

Applying phosphate-solubilizing bacteria (PSB) as biofertilizers has enormous potential for sustainable agriculture. Despite this, there is still a lack of information regarding the expression of key genes related to phosphate-solubilization (PS) and efficient formulation strategies. In this study, we investigated rock PS by Ochrobactrum sp. SSR (DSM 109610) by relating it to bacterial gene expression and searching for an efficient formulation. The quantitative PCR (qPCR) primers were designed for PS marker genes glucose dehydrogenase (gcd), pyrroloquinoline quinone biosynthesis protein C (pqqC), and phosphatase (pho). The SSR-inoculated soil supplemented with rock phosphate (RP) showed a 6-fold higher expression of pqqC and pho compared to inoculated soil without RP. Additionally, an increase in plant phosphorous (P) (2%), available soil P (4.7%), and alkaline phosphatase (6%) activity was observed in PSB-inoculated plants supplemented with RP. The root architecture improved by SSR, with higher root length, diameter, and volume. Ochrobactrum sp. SSR was further used to design bioformulations with two well-characterized PS, Enterobacter spp. DSM 109592 and DSM 109593, using the four organic amendments, biochar, compost, filter mud (FM), and humic acid. All four carrier materials maintained adequate survival and inoculum shelf life of the bacterium, as indicated by the field emission scanning electron microscopy analysis. The FM-based bioformulation was most efficacious and enhanced not only wheat grain yield (4-9%) but also seed P (9%). Moreover, FM-based bioformulation enhanced soil available P (8.5-11%) and phosphatase activity (4-5%). Positive correlations were observed between the PSB solubilization in the presence of different insoluble P sources, and soil available P, soil phosphatase activity, seed P content, and grain yield of the field grown inoculated wheat variety Faisalabad-2008, when di-ammonium phosphate fertilizer application was reduced by 20%. This study reports for the first time the marker gene expression of an inoculated PSB strain and provides a valuable groundwork to design field scale formulations that can maintain inoculum dynamics and increase its shelf life. This may constitute a step-change in the sustainable cultivation of wheat under the P-deficient soil conditions.

Diversity and Phosphate Solubilization Efficiency of Phosphate Solubilizing Bacteria Isolated from Semi-Arid Agroecosystems of Eastern Kenya

Phosphorus (P) is a major nutrient required for plant growth but it forms complexes with other elements in soil upon application. A cost-effective way of availing P to plants is by use of Phosphate Solubilizing Bacteria (PSB). There is a wide range of PSB suited for diverse agro-ecologies. A large part of Eastern Kenya especially the lower altitude regions are semi-arid with nutrient depleted soils and predominated by low-income smallholders farmers who do not afford costly inorganic fertilizers. To alleviate poor soil nutrition in this agroecosystem, we sought to study the diversity of phosphate solubilizing bacteria and their phosphate solubilization efficiency. The bacteria were selectively isolated in Pikovskaya’s agar media. Bacterial colonies were enumerated as Colony Forming Units and morphological characterization determined by analyzing morphological characteristics. Genetic characterization was determined based on sequencing of 16S rRNA. A total of 71 PSB were isolated and they were placed into 23 morphological groups. Correlation analysis showed a negative correlation between phosphate solubilizing bacteria and the levels of phosphorus, iron, calcium, magnesium and soil pH. Analysis of 16S rRNA sequences revealed that the genetic sequences of the isolates matched the strains from the genera Burkholderia, Pseudomonas, Bacillus, Enterobacter, Pantoea, Paraburkholderia, Cronobacter, Ralstonia, Curtobacterium, and Massilia deposited in NCBI Database. Analysis of Molecular Variance showed that variation within populations was higher than that of among populations. Phosphate solubilization index values ranged between 1.143 and 5.883. Findings on biodiversity of phosphate solubilizing bacteria led to identification of 10 candidate isolates for plant growth improvement and subsequently, bio-fertilizer development.

Bacillus subtilis Impact on Plant Growth, Soil Health and Environment: Dr. Jekyll and Mr. Hyde

The increased dependence of farmers on chemical fertilizers poses a risk to soil fertility and ecosystem stability. Plant growth-promoting rhizobacteria (PGPR) are at the forefront of sustainable agriculture, providing multiple benefits for the enhancement of crop production and soil health. Bacillus subtilis is a common PGPR in soil that plays a key role in conferring biotic and abiotic stress tolerance to plants by induced systemic resistance (ISR), biofilm formation, and lipopeptide production. As a part of bioremediating technologies, Bacillus spp. can purify metal contaminated soil. It acts as a potent denitrifying agent in agroecosystems while improving the carbon sequestration process when applied in a regulated concentration. Although it harbors several antibiotic resistance genes (ARGs), it can reduce the horizontal transfer of ARGs during manure composting by modifying the genetic makeup of existing microbiota. In some instances, it affects the beneficial microbes of the rhizosphere. External inoculation of B. subtilis has both positive and negative impacts on the endophytic and semi-synthetic microbial community. Soil texture, type, pH, and bacterial concentration play a crucial role in the regulation of all these processes. Soil amendments and microbial consortia of Bacillus produced by microbial engineering could be used to lessen the negative effect on soil microbial diversity. The complex plant-microbe interactions could be decoded using transcriptomics, proteomics, metabolomics, and epigenomics strategies which would be beneficial for both crop productivity and the well-being of soil microbiota. Bacillus subtilis has more positive attributes similar to the character of Dr. Jekyll and some negative attributes on plant growth, soil health, and the environment akin to the character of Mr. Hyde.

Phosphate Solubilizing Microorganism Bacillus sp. MVY-004 and Its Significance for Biomineral Fertilizers' Development in Agrobiotechnology

In this study, a phosphate solubilizing microorganism was isolated from the soil of an agricultural field in Lithuania. Based on 16S rRNA gene sequence analysis, the strain was identified as Bacillus sp. and submitted to the NCBI database, Sector of Applied Bio-catalysis, University Institute of Biotechnology, Vilnius, Lithuania and allocated the accession number KY882273. The Bacillus sp. was assigned with the number MVY-004. The culture nutrient medium and growth conditions were optimized: molasses was used as a carbon source; yeast extract powder was used as an organic source; NH₄H₂PO₄ was used as a nitrogen source; the culture growth temperature was 30 ± 0.5 °C; the initial value of pH was 7.0 ± 0.5; the partial pressure of oxygen (pO₂) was 60 ± 2.0; the mixer revolutions per minute (RPM) were 25-850, and the incubation and the fermentation time was 48-50 h. Analysis using Liquid Chromatography Time-of-Flight Mass Spectrometry (LC-TOF/MS) results showed that Bacillus sp. MVY-004 produced organic acids such as citric, succinic, 2-ketogluconic, gluconic, malic, lactic, and oxalic acids. Furthermore, the experiment showed that Bacillus sp. MVY-004 can also produce the following phytohormones: indole-3-acetic (IAA), jasmonic (JA), and gibberellic (GA3) acids. In the climate chamber, the experiment was performed using mineral fertilizer (NPS-12:40:10 80 Kg ha^-1) and mineral fertilizers in combination with Bacillus sp. MVY-004 cells (NPS-12:40:10 80 Kg ha^-1 + Bacillus sp. MVY-004) in loamy soil. Analysis was performed in three climate conditions: normal (T = 20 °C; relative humidity 60%); hot and dry (T = 30 °C; relative humidity 30%); hot and humid (T = 30 °C; relative humidity 80%).

Biofertilizers: An ecofriendly technology for nutrient recycling and environmental sustainability

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Agriculture plays an important role in a country's economy. In modern intensive agricultural practices, chemical fertilizers and pesticides are applied on large scale to increase crop production in order to meet the nutritional requirements of the ever-increasing world population. However, rapid urbanization with shrinking agricultural lands, dramatic change in climatic conditions and extensive use of agrochemicals in agricultural practices has been found to cause environmental disturbances and public health hazards affecting food security and sustainability in agriculture. Besides this, agriculture soils are continuously losing their quality and physical properties as well as their chemical (imbalance of nutrients) and biological health due to indiscriminate use of agrochemicals. Plant-associated microbes with their plant growth- promoting traits have enormous potential to solve these challenges and play a crucial role in enhancing plant biomass and crop yield under greenhouse and field conditions. The beneficial mechanisms of plant growth improvement include enhanced availability of nutrients (i.e., N, P, K, Zn and S), phytohormone modulation, biocontrol of phytopathogens and amelioration of biotic and abiotic stresses. This plant-microbe interplay is indispensable for sustainable agriculture and these microbes may perform essential role as an ecological engineer to reduce the use of chemical fertilizers. Various steps involved for production of solid-based or liquid biofertilizer formulation include inoculum preparation, addition of cell protectants such as glycerol, lactose, starch, a good carrier material, proper packaging and best delivery methods. In addition, recent developments of formulation include entrapment/microencapsulation, nano-immobilization of microbial bioinoculants and biofilm-based biofertilizers. Thus, inoculation with beneficial microbes has emerged as an innovative eco-friendly technology to feed global population with available resources. This review critically examines the current state-of-art on use of microbial strains as biofertilizers in different crop systems for sustainable agriculture and in maintaining soil fertility and enhancing crop productivity. It is believed that acquisition of advanced knowledge of plant-PGPR interactions, bioengineering of microbial communities to improve the performance of biofertilizers under field conditions, will help in devising strategies for sustainable, environment-friendly and climate smart agricultural technologies to deliver short and long terms solutions for improving crop productivity to feed the world in a more sustainable manner.

Modern intensive agricultural practices face numerous challenges that pose major threats to global food security. In order to address the nutritional requirements of the ever-increasing world population, chemical fertilizers and pesticides are applied on large scale to increase crop production. However, the injudicious use of agrochemicals has resulted in environmental pollution leading to public health hazards. Moreover, agriculture soils are continuously losing their quality and physical properties as well as their chemical (imbalance of nutrients) and biological health. Plant-associated microbes with their plant growth- promoting traits have enormous potential to solve these challenges and play a crucial role in enhancing plant biomass and crop yield. The beneficial mechanisms of plant growth improvement include enhanced nutrient availability, phytohormone modulation, biocontrol of phytopathogens and amelioration of biotic and abiotic stresses. Solid-based or liquid bioinoculant formulation comprises inoculum preparation, addition of cell protectants such as glycerol, lactose, starch, a good carrier material, proper packaging and best delivery methods. Recent developments of formulation include entrapment/microencapsulation, nano-immobilization of microbial bioinoculants and biofilm-based biofertilizers. This review critically examines the current state-of-art on use of microbial strains as biofertilizers and the important roles performed by these beneficial microbes in maintaining soil fertility and enhancing crop productivity.

Phosphorus-arsenic interaction in the 'soil-plant-microbe' system and its influence on arsenic pollution

Elevated arsenic (As) in soil is of public concern due to the carcinogenicity. Phosphorus (P) strongly influences the adsorption, absorption, transport, and transformation of As in the soil and in organisms due to the similarity of the chemical properties of P and As. In soil, P, particularly inorganic P, can release soil-retained As (mostly arsenate) by competing for adsorption sites. In plant and microbial systems, P usually reduces As (mainly arsenate) uptake and affects As biotransformation by competing for As transporters. The intensity and pattern of PAs interaction are highly dependent on the forms of As and P, and strongly influenced by various biotic and abiotic factors. An understanding of the PAs interaction in 'soil-plant-microbe' systems is of great value to prevent soil As from entering the human food chain. Here, we review PAs interactions and the main influential factors in soil, plant, and microbial subsystems and their effects on the As release, absorption, transformation, and transport in the 'soil-plant-microbe' system. We also analyze the application potential of P fertilization as a control for As pollution and suggest the research directions that need to be followed in the future.

Sorghum-Phosphate Solubilizers Interactions: Crop Nutrition, Biotic Stress Alleviation, and Yield Optimization

Sweet sorghum [Sorghum bicolor (L.) Moench] is a highly productive, gluten-free cereal crop plant that can be used as an alternative energy resource, human food, and livestock feed or for biofuel-ethanol production. Phosphate fertilization is a common practice to optimize sorghum yield but because of high cost, environmental hazards, and soil fertility reduction, the use of chemical P fertilizer is discouraged. Due to this, the impetus to search for an inexpensive and eco-friendly microbiome as an alternative to chemical P biofertilizer has been increased. Microbial formulations, especially phosphate solubilizing microbiome (PSM) either alone or in synergism with other rhizobacteria, modify the soil nutrient pool and augment the growth, P nutrition, and yield of sorghum. The use of PSM in sorghum disease management reduces the dependence on pesticides employed to control the phytopathogens damage. The role of PSM in the sorghum cultivation system is, however, relatively unresearched. In this manuscript, the diversity and the strategies adopted by PSM to expedite sorghum yield are reviewed, including the nutritional importance of sorghum in human health and the mechanism of P solubilization by PSM. Also, the impact of solo or composite inoculations of biological enhancers (PSM) with nitrogen fixers or arbuscular mycorrhizal fungi is explained. The approaches employed by PSM to control sorghum phytopathogens are highlighted. The simultaneous bio-enhancing and biocontrol activity of the PS microbiome provides better options for the replacement of chemical P fertilizers and pesticide application in sustainable sorghum production practices.

Establishment of Ailanthus tryphysa (Dennst.) Alston inoculated with beneficial microbes in barren laterite rocks

Developing countries including India are using laterite bricks extracted from laterite rocks for building construction. Laterite rocks are found barren usually as they are not fit for cultivation. Extraction of laterite bricks from these barren laterite rocks causing land degradation and posing environmental threats in the laterite excavated lands. Hence, planting or establishing of trees on laterite rocks can prevent land degradation and environmental problems. In this study, it was decided to establish Ailanthus tryphysa (Dennst.) Alston a multipurpose native tree species of India on laterite rocks with suitable beneficial microbes as growth promotors. The laterite soils dug out from laterite rocks were tested and found that the soils have lack of beneficial microbes and poor in major nutrients (N, P, K). Therefore the beneficial microbes, arbuscular mycorrhizal fungi and growth promoting bacteria were used for A. tryphysa as they are one of the important soil properties. The laterite soils were also used as potting media for the seedlings of A. tryphysa in nursery and thereafter the cultured beneficial microbes were inoculated in to the seedlings and maintained for three months. After three months the seedlings were planted at laterite rocks and monitored for their growth and survival. The results of the experiment showed that beneficial microbes inoculated seedlings improved the growth, biomass, tissue nutrient content and 95% of survival rate after twelve months in laterite rocks. These results confirmed that the beneficial microbes have successfully established the A. tryphysa seedlings in laterite rocks through transfer of essential nutrients.

Bacillus sp. and arbuscular mycorrhizal fungi consortia enhance wheat nutrient and yield in the second-year field trial: Superior performance in comparison with chemical fertilizers

AIMS

The aim of the study is to analyse the effect of microbial consortia for wheat biofortification, growth, yield and soil fertility as part of a 2-year field study and compare it with the use of chemical fertilizers.

METHODS AND RESULTS

A field trial (second year) was conducted with various combinations of plant growth-promoting bacteria (PGPB) and arbuscular mycorrhizal fungi (AMF) treatments, ranging from a single inoculant to multiple combinations. The microbial consortia used were Bacillus sp. and AMF based on first-year field trial results. The consortia based on native (CP4) and non-native (AHP3) PGPB (Bacillus sp.) and AMF performed better in terms of nutrients content in wheat grain tissue and yield-related traits compared with chemical fertilizer treated and untreated control. Dual treatment of PGPB (CP4+AHP3) combined with AMF resulted in a significant increase in antioxidants. The spatial colonization of AMF in roots indicated that both the isolates CP4 and AHP3 were able to enhance the AMF colonization in root tissue. Furthermore, soil enzymes' activities were higher with the PGPB and AMF combination giving the best results. A positive correlation was recorded between plant growth, grain yield and soil physicochemical parameters.

CONCLUSIONS

Our findings confirm that the combined treatment of CP4 and AHP3 and AMF functions as an effective microbial consortium with excellent application prospects for wheat biofortification, grain yield and soil fertility compared with chemical fertilizers.

SIGNIFICANCE AND IMPACT OF STUDY

The extensive application of chemical fertilizers on low-yielding field sites is a severe concern for cereal crops, especially wheat in the Asian continent. This study serves as a primer for implementing site-specific sustainable agricultural-management practices using a green technology leading to significant gains in agriculture.

Drought Tolerant Enterobacter sp./Leclercia adecarboxylata Secretes Indole-3-acetic Acid and Other Biomolecules and Enhances the Biological Attributes of Vigna radiata (L.) R. Wilczek in Water Deficit Conditions

Drought or water stress is a limiting factor that hampers the growth and yield of edible crops. Drought-tolerant plant growth-promoting rhizobacteria (PGPR) can mitigate water stress in crops by synthesizing multiple bioactive molecules. Here, strain PAB19 recovered from rhizospheric soil was biochemically and molecularly characterized, and identified as Enterobacter sp./Leclercia adecarboxylata (MT672579.1). Strain PAB19 tolerated an exceptionally high level of drought (18% PEG-6000) and produced indole-3-acetic acid (176.2 ± 5.6 µg mL-1), ACC deaminase (56.6 ± 5.0 µg mL-1), salicylic acid (42.5 ± 3.0 µg mL-1), 2,3-dihydroxy benzoic acid (DHBA) (44.3 ± 2.3 µg mL-1), exopolysaccharide (204 ± 14.7 µg mL-1), alginate (82.3 ± 6.5 µg mL-1), and solubilized tricalcium phosphate (98.3 ± 3.5 µg mL-1), in the presence of 15% polyethylene glycol. Furthermore, strain PAB19 alleviated water stress and significantly (p ≤ 0.05) improved the overall growth and biochemical attributes of Vigna radiata (L.) R. Wilczek. For instance, at 2% PEG stress, PAB19 inoculation maximally increased germination, root dry biomass, leaf carotenoid content, nodule biomass, leghaemoglobin (LHb) content, leaf water potential (ΨL), membrane stability index (MSI), and pod yield by 10%, 7%, 14%, 38%, 9%, 17%, 11%, and 11%, respectively, over un-inoculated plants. Additionally, PAB19 inoculation reduced two stressor metabolites, proline and malondialdehyde, and antioxidant enzymes (POD, SOD, CAT, and GR) levels in V. radiata foliage in water stress conditions. Following inoculation of strain PAB19 with 15% PEG in soil, stomatal conductance, intercellular CO2 concentration, transpiration rate, water vapor deficit, intrinsic water use efficiency, and photosynthetic rate were significantly improved by 12%, 8%, 42%, 10%, 9% and 16%, respectively. Rhizospheric CFU counts of PAB19 were 2.33 and 2.11 log CFU g-1 after treatment with 15% PEG solution and 8.46 and 6.67 log CFU g-1 for untreated controls at 40 and 80 DAS, respectively. Conclusively, this study suggests the potential of Enterobacter sp./L. adecarboxylata PAB19 to alleviate water stress by improving the biological and biochemical features and of V. radiata under water-deficit conditions.

Impacts of Effective Microorganisms, Compost Tea, Fulvic Acid, Yeast Extract, and Foliar Spray with Seaweed Extract on Sweet Pepper Plants under Greenhouse Conditions

Sweet pepperincludes several vitamins and is regarded as a great source of bioactive nutrients, such as carotenoids and phenolic compounds, for human growth and activities. This work aimed to investigate the effects of the soil addition of growth stimulants, namely, effective microorganisms (EM), compost tea, fulvic acid, and yeast extract, and foliar applications of seaweed extract, on the vegetative growth, enzyme activity, phytohormones content, chemical constituents of plant foliage, fruit yield, and fruit quality of sweet pepper plants (Capsicum annuum L. cv. Zidenka) growing under greenhouse conditions. The results showed that the tallest plant, largest leaf area/plant, and heaviest plant fresh and dry weights were recorded after combining a soil addition of yeast extract and foliar spray with seaweed extracts at 3 g/L in two growing seasons. The highest number of fruit/plant, fruit yield/m², fruit values of vitamin C (VC), total sugars, total soluble solids (TSS), and carotenoids, along with the highest leaf of cytokines, P, K, Fe, and total carbohydrates values, were obtained using a soil addition of fulvic acid and spray with seaweed extract at 3 g/L in the two seasons of study. These treatments also provided the lowest abscisic acid, peroxidase, and super oxidase dismutase values in the same conditions. Sweet pepper plants supplemented with compost tea and seaweed extract foliar spray at 3 g/L were the most promising for inducing the highest values of fruit fresh and dry weights, fruit length and diameter, and the leavesrichest in N, Zn, and Mn; inversely, it induced the lowest catalase levels in both seasons. The applications of EM, yeast extract, and seaweed extract could be applied for high growth, mineral levels, enzymatic activity, fruit yield, and nutritional value of sweet pepper fruit and minimizing environmental pollution.

Effect of Treating Acid Sulfate Soils with Phosphate Solubilizing Bacteria on Germination and Growth of Tomato (Lycopersicon esculentum L.)

Acid sulfate soils contain sulfide minerals that have adverse environmental effects because they can lead to acidic drainage and prevent the establishment of vegetation. The current study examined the effect of a novel method for the restoration of these soils and the promotion of germination and plant growth. Thus, we isolated two strains of phosphate solubilizing bacteria, Methylobacterium sp. PS and Caballeronia sp. EK, characterized their properties, and examined their effects in promoting the growth of tomato plants (Lycopersicon esculentum L.) in acid sulfate soil. Compared with untreated control soil, treatment of acid sulfate soils with these bacterial strains led to increased seed germination, growth of plants with more leaves, and plants with greater levels of total-adenosine tri-phosphate (tATP). Relative to the untreated control soil, the addition of Caballeronia sp. EK led to a 60% increase in seed germination after 52 days, growth of plants with more than 3 times as many leaves, and a 45.2% increase in tATP after 50 days. This strain has potential for use as a plant biofertilizer that promotes vegetation growth in acid sulfate soils by improving the absorption of phosphorous.

Bioformulation of Silk-Based Coating to Preserve and Deliver Rhizobium tropici to Phaseolus vulgaris Under Saline Environments

Seed priming has been for a long time an efficient application method of biofertilizers and biocontrol agents. Due to the quick degradation of the priming agents, this technique has been limited to specific immediate uses. With the increase of awareness of the importance of sustainable use of biofertilizers, seed coating has presented a competitive advantage regarding its ability to adhere easily to the seed, preserve the inoculant, and decompose in the soil. This study compared primed Phaseolus vulgaris seeds with Rhizobium tropici and trehalose with coated seeds using a silk solution mixed with R. tropici and trehalose. We represented the effect of priming and seed coating on seed germination and the development of seedlings by evaluating physiological and morphological parameters under different salinity levels (0, 20, 50, and 75 mM). Results showed that germination and morphological parameters have been significantly enhanced by applying R. tropici and trehalose. Seedlings of coated seeds show higher root density than the freshly primed seeds and the control. The physiological response has been evaluated through the stomatal conductance, the chlorophyll content, and the total phenolic compounds. The stability of these physiological traits indicated the role of trehalose in the protection of the photosystems of the plant under low and medium salinity levels. R. tropici and trehalose helped the plant mitigate the negative impact of salt stress on all traits. These findings represent an essential contribution to our understanding of stress responses in coated and primed seeds. This knowledge is essential to the design of coating materials optimized for stressed environments. However, further progress in this area of research must anticipate the development of coatings adapted to different stresses using micro and macro elements, bacteria, and fungi with a significant focus on biopolymers for sustainable agriculture and soil microbiome preservation.

Enabling sustainable agriculture through understanding and enhancement of microbiomes

Harnessing plant-associated microbiomes offers an invaluable strategy to help agricultural production become more sustainable while also meeting growing demands for food, feed and fiber. A plethora of interconnected interactions among the host, environment and microbes, occurring both above and below ground, drive recognition, recruitment and colonization of plant-associated microbes, resulting in activation of downstream host responses and functionality. Dissecting these complex interactions by integrating multiomic approaches, high-throughput culturing, and computational and synthetic biology advances is providing deeper understanding of the structure and function of native microbial communities. Such insights are paving the way towards development of microbial products as well as microbiomes engineered with synthetic microbial communities capable of delivering agronomic solutions. While there is a growing market for microbial-based solutions to improve crop productivity, challenges with commercialization of these products remain. The continued translation of plant-associated microbiome knowledge into real-world scenarios will require concerted transdisciplinary research, cross-training of a next generation of scientists, and targeted educational efforts to prime growers and the general public for successful adoption of these innovative technologies.

Potential Use of Beneficial Microorganisms for Soil Amelioration, Phytopathogen Biocontrol, and Sustainable Crop Production in Smallholder Agroecosystems

Smallholder agroecosystems play a key role in the world's food security providing more than 50% of the food produced globally. These unique agroecosystems face a myriad of challenges and remain largely unsupported, yet they are thought to be a critical resource for feeding the projected increasing human population in the coming years. The new challenge to increase food production through agricultural intensification in shrinking per capita arable lands, dwindling world economies, and unpredictable climate change, has led to over-dependence on agrochemical inputs that are often costly and hazardous to both human and animal health and the environment. To ensure healthy crop production approaches, the search for alternative ecofriendly strategies that best fit to the smallholder systems have been proposed. The most common and widely accepted solution that has gained a lot of interest among researchers and smallholder farmers is the use of biological agents; mainly plant growth promoting microorganisms (PGPMs) that provide essential agroecosystem services within a holistic vision of enhancing farm productivity and environmental protection. PGPMs play critical roles in agroecological cycles fundamental for soil nutrient amelioration, crop nutrient improvement, plant tolerance to biotic and abiotic stresses, biocontrol of pests and diseases, and water uptake. This review explores different research strategies involving the use of beneficial microorganisms, within the unique context of smallholder agroecosystems, to promote sustainable maintenance of plant and soil health and enhance agroecosystem resilience against unpredictable climatic perturbations.

Isolation and Characterization of Phosphate Solubilizing Streptomyces sp. Endemic from Sugar Beet Fields of the Beni-Mellal Region in Morocco

In the course of our research, aimed at improving sugar beets phosphorus nutrition, we isolated and characterized Streptomyces sp. strains, endemic from sugar beet fields of the Beni-Mellal region, which are able to use natural rock phosphate (RP) and tricalcium phosphate (TCP) as sole phosphate sources. Ten Streptomyces sp. isolates yielded a comparable biomass in the presence of these two insoluble phosphate sources, indicating that they were able to extract similar amount of phosphorus (P) from the latter for their own growth. Interestingly, five strains released soluble P in large excess from TCP in their culture broth whereas only two strains, BP, related to Streptomyces bellus and BYC, related to Streptomyces enissocaesilis, released a higher or similar amount of soluble P from RP than from TCP, respectively. This indicated that the rate of P released from these insoluble phosphate sources exceeded its consumption rate for bacterial growth and that most strains solubilized TCP more efficiently than RP. Preliminary results suggested that the solubilization process of BYC, the most efficient RP and TCP solubilizing strain, involves both acidification of the medium and excretion of siderophores. Actinomycete strains possessing such interesting RP solubilizing abilities may constitute a novel kind of fertilizers beneficial for plant nutrition and more environmentally friendly than chemical fertilizers in current use.

An Actinobacterium Strain From Soil of Cerrado Promotes Phosphorus Solubilization and Plant Growth in Soybean Plants

The huge biological diversity of the Brazilian Cerrado is an important source of economically interesting microbial agents. The phylum Actinobacteria plays an important role in nutrient cycling, potentially improving their availability to plants. In this study, we isolated an actinobacteria (strain 3AS4) from wheat rhizospheres of crops cultivated in the Cerrado biome. Strain 3AS4 was identified as belonging to the genus Streptomyces and had phosphorus mobilization ability, mineralizing approximately 410 μg ml^–1 from phytate, 300 μg ml^–1 from calcium phosphate, and 200 μg ml^–1 from rock phosphate. The analysis of the actinobacteria crude extract by spectrometric techniques revealed the presence of gluconic and 2-ketogluconic acid, and a greenhouse experiment was carried out to evaluate its plant growth promotion activity in soybean. Soil in its natural condition (with no phosphorus addition), 40 kg ha^–1 rock phosphate from Bayovar (RP) added to soil, and triple super phosphate (SPT) added to soil were used. Significant differences in plant height were observed at 6 weeks when the plants were inoculated with the 3AS4 strain. The growth of inoculated plants in natural condition was promoted in 17% compared with the RP and SPT non-inoculated conditions, suggesting that inoculation can enable plants to grow with lower chemical P fertilizers. In the plants that were inoculated with the 3AS4 strain in the RP condition, the plant height increased by approximately 80% and the shoot:root ratio was approximately 30% higher compared to control conditions (non-inoculated plants in natural conditions). 3AS4 has P-solubilizing potential and can be exploited as an inoculant for soybean cultivation. These results suggest that this actinobacterium is a valuable resource for sustainable agriculture and will allow the reduction of phosphate fertilization in the future.

New developments in biological phosphorus accessibility and recovery approaches from soil and waste streams

Phosphorus (P) is a non-renewable resource and is on the European Union's list of critical raw materials. It is predicted that the P consumption peak will occur in the next 10 to 20 years. Therefore, there is an urgent need to find accessible sources in the immediate environment, such as soil, and to use alternative resources of P such as waste streams. While enormous progress has been made in chemical P recovery technologies, most biological technologies for P recovery are still in the developmental stage and are not reaching industrial application. Nevertheless, biological P recovery could offer good solutions as these technologies can return P to the human P cycle in an environmentally friendly way. This mini-review provides an overview of the latest approaches to make P available in soil and to recover P from plant residues, animal and human waste streams by exploiting the universal trait of P accumulation and P turnover in microorganisms and plants.

The Screening of Potassium- and Phosphate-Solubilizing Actinobacteria and the Assessment of Their Ability to Promote Wheat Growth Parameters

Soil fertility and plant nutrition require an adequate management of essential macronutrients such as potassium (K) and phosphorus (P), which are mandatory for plant development. Bioleaching of K and P bearing minerals improves their chemical weathering and increases the performance of the biofertilization strategies. In this study, in vitro and greenhouse experiments were carried out to investigate P and K solubilization traits of nine Actinobacteria (P13, P14, P15, P16, P17, P18, BC3, BC10, and BC11) under fertilization with rock phosphate (RP). K and P solubilization were evaluated on Alexandrov and NBRIP media containing mica and six RP samples, respectively. The actinobacterial strains were able to solubilize K in Alexandrov medium supplemented with RP. However, when soluble P was used instead of RP, only four strains of Actinobacteria (Streptomyces alboviridis P18–Streptomyces griseorubens BC3–Streptomyces griseorubens BC10 and Nocardiopsis alba BC11) solubilized K. The solubilization values of K ranged from 2.6 to 41.45 mg/L while those of P varied from 0.1 to 32 mg/L. Moreover, all strains were able to produce IAA, siderophore, HCN, and ammonia and significantly improved the germination rate and the vigor index of wheat. The pot experiments revealed that four strains (Streptomyces alboviridis P18, Streptomyces griseorubens BC3, Streptomyces griseorubens BC10, and Nocardiopsis alba BC11) significantly improved the growth parameters of wheat, namely root length (1.75–23.84%), root volume (41.57–71.46%), root dry weight (46.89–162.41%), shoot length (8.92–23.56%), and shoot dry weight (2.56–65.68%) compared to the uninoculated control. These findings showed that Streptomyces griseorubens BC10 and Nocardiopsis alba BC11 are promising candidates for the implementation of efficient biofertilization strategies to improve soil fertility and plant yield under rock P and rock K fertilization.

Rethinking Crop Nutrition in Times of Modern Microbiology: Innovative Biofertilizer Technologies

Global population growth poses a threat to food security in an era of increased ecosystem degradation, climate change, soil erosion, and biodiversity loss. In this context, harnessing naturally-occurring processes such as those provided by soil and plant-associated microorganisms presents a promising strategy to reduce dependency on agrochemicals. Biofertilizers are living microbes that enhance plant nutrition by either by mobilizing or increasing nutrient availability in soils. Various microbial taxa including beneficial bacteria and fungi are currently used as biofertilizers, as they successfully colonize the rhizosphere, rhizoplane or root interior. Despite their great potential to improve soil fertility, biofertilizers have yet to replace conventional chemical fertilizers in commercial agriculture. In the last 10 years, multi-omics studies have made a significant step forward in understanding the drivers, roles, processes, and mechanisms in the plant microbiome. However, translating this knowledge on microbiome functions in order to capitalize on plant nutrition in agroecosystems still remains a challenge. Here, we address the key factors limiting successful field applications of biofertilizers and suggest potential solutions based on emerging strategies for product development. Finally, we discuss the importance of biosafety guidelines and propose new avenues of research for biofertilizer development.

A Molecule of the Viridomycin Family Originating from a Streptomyces griseus-Related Strain Has the Ability to Solubilize Rock Phosphate and to Inhibit Microbial Growth

Some soil-borne microorganisms are known to have the ability to solubilize insoluble rock phosphate and this process often involves the excretion of organic acids. In this issue, we describe the characterization of a novel solubilizing mechanism used by a Streptomyces strain related to Streptomyces griseus isolated from Moroccan phosphate mines. This process involves the excretion of a compound belonging to the viridomycin family that was shown to play a major role in the rock phosphate bio weathering process. We propose that the chelation of the positively charged counter ions of phosphate constitutive of rock phosphate by this molecule leads to the destabilization of the structure of rock phosphate. This would result in the solubilization of the negatively charged phosphates, making them available for plant nutrition. Furthermore, this compound was shown to inhibit growth of fungi and Gram positive bacteria, and this antibiotic activity might be due to its strong ability to chelate iron, a metallic ion indispensable for microbial growth. Considering its interesting properties, this metabolite or strains producing it could contribute to the development of sustainable agriculture acting as a novel type of slow release bio-phosphate fertilizer that has also the interesting ability to limit the growth of some common plant pathogens.

Bioremediation potential of new cadmium, chromium, and nickel-resistant bacteria isolated from tropical agricultural soil

Soil management using fertilizers can modify soil chemical, biochemical and biological properties, including the concentration of trace-elements as cadmium (Cd), chromium (Cd) and nickel (Ni). Bacterial isolates from Cd, Cr, and Ni-contaminated soil were evaluated for some characteristics for their use in bioremediation. Isolates (592) were obtained from soil samples (19) of three areas used in three maize cultivation systems: no-tillage and conventional tillage with the application of mineral fertilizers; minimum tillage with the application of sewage sludge. Four isolates were resistant to Cr³⁺ (3.06 mmol dm^-3) and Cd²⁺ (2.92 mmol dm^-3). One isolate was resistant to the three metals at 0.95 mmol dm^-3. All isolates developed in a medium of Cd²⁺, Cr³⁺ and Ni²⁺ at 0.5 mmol dm^-3, and removed Cd²⁺ (17-33%) and Cr⁶⁺ (60-70%). They were identified by sequencing of the gene 16S rRNA, as bacteria of the genera Paenibacillus, Burkholderia, Ensifer, and two Cupriavidus. One of the Cupriavidus isolate was able to remove 60% of Cr⁶⁺ from the culture medium and showed high indole acetic acid production capacity. We evaluated it in a microbe-plant system that could potentially be deployed in bioremediation by removing toxic metals from contaminated soil.

Bioprospecting plant growth promoting endophytic bacteria isolated from Himalayan yew (Taxus wallichiana Zucc.)

The present study aims to investigate the endophytic bacteria, isolated from the roots of Taxus wallichiana Zucc. and designated as GBPI_TWL and GBPI_TWr, for their plant growth promoting traits. On the basis of phenotypic and molecular characters, the bacteria are identified as species of Burkholderia and Enterobacter, respectively. Both the bacteria could grow at wide range of temperature (5-40 °C, opt=25 °C) and pH (1.5-11.0, opt = 6-7), and tolerate salt concentration up to 12 %. While both the bacterial endophytes possessed siderophore, HCN, ammonia, and salicyclic acid producing abilities, GBPI_TWL showed IAA and ACC deaminase producing abilities, in addition. The bacteria were found to be potential phosphate solubilizers at wide temperature range (5-35 °C) by utilizing tricalcium, iron, and aluminium phosphate as substrate. Further, the bacterial isolates produced phytase and phosphatase enzymes in both acidic and alkaline conditions. Positive influence of the inoculation with the bioformulations of GBPI_TWL and GBPI_TWr was demonstrated on the test crops namely rice (Oryza sativa) and soybean (Glycine max) with respect to physico-chemical and plant growth parameters in net house experiments. The study will have implications in developing bioformulations, specifically for low temperature environments, in view of environmental sustainability.

Current perspectives and applications in plant probiotics

As agriculture and food security face unprecedented challenges, emerging agricultural innovations and existing practices require ongoing examination in the context of sustainability. In this review, we focus on the use of probiotic microorganisms for improved plant production. As plants are enormously diverse, emphasis is placed on the fundamental sites of plant-microbe interactions regarding benefits and challenges encountered when altering the microbiome of these locations. The soil, the external plant epidermis, and internal plant tissue are considered in discussion regarding the type of plant probiotic application. Plant probiotics range from broader soil beneficial microorganisms (such as Trichoderma spp.) through to specialised epiphytes and endophytes (such as root nodule bacteria). As each site of interaction affects plant growth differently, potential outcomes from the introduction of these exogenous microorganisms are discussed with regard to plant productivity. Finally, recommendations regarding regulation and future use of plant probiotics are points of consideration throughout this review.