Multifunctional properties of phosphate-solubilizing microorganisms grown on agro-industrial wastes in fermentation and soil conditions

Fungi, P-Solubilization, and Plant Nutrition

The application of plant beneficial microorganisms is widely accepted as an efficient alternative to chemical fertilizers and pesticides. It was shown that annually, mycorrhizal fungi and nitrogen-fixing bacteria are responsible for 5 to 80% of all nitrogen, and up to 75% of P plant acquisition. However, while bacteria are the most studied soil microorganisms and most frequently reported in the scientific literature, the role of fungi is relatively understudied, although they are the primary organic matter decomposers and govern soil carbon and other elements, including P-cycling. Many fungi can solubilize insoluble phosphates or facilitate P-acquisition by plants and, therefore, form an important part of the commercial microbial products, with Aspergillus, Penicillium and Trichoderma being the most efficient. In this paper, the role of fungi in P-solubilization and plant nutrition will be presented with a special emphasis on their production and application. Although this topic has been repeatedly reviewed, some recent views questioned the efficacy of the microbial P-solubilizers in soil. Here, we will try to summarize the proven facts but also discuss further lines of research that may clarify our doubts in this field or open new perspectives on using the microbial and particularly fungal P-solubilizing potential in accordance with the principles of the sustainability and circular economy.

Psychrophilic Bacterial Phosphate-Biofertilizers: A Novel Extremophile for Sustainable Crop Production under Cold Environment

Abiotic stresses, including low-temperature environments, adversely affect the structure, composition, and physiological activities of soil microbiomes. Also, low temperatures disturb physiological and metabolic processes, leading to major crop losses worldwide. Extreme cold temperature habitats are, however, an interesting source of psychrophilic and psychrotolerant phosphate solubilizing bacteria (PSB) that can ameliorate the low-temperature conditions while maintaining their physiological activities. The production of antifreeze proteins and expression of stress-induced genes at low temperatures favors the survival of such organisms during cold stress. The ability to facilitate plant growth by supplying a major plant nutrient, phosphorus, in P-deficient soil is one of the novel functional properties of cold-tolerant PSB. By contrast, plants growing under stress conditions require cold-tolerant rhizosphere bacteria to enhance their performance. To this end, the use of psychrophilic PSB formulations has been found effective in yield optimization under temperature-stressed conditions. Most of the research has been done on microbial P biofertilizers impacting plant growth under normal cultivation practices but little attention has been paid to the plant growth-promoting activities of cold-tolerant PSB on crops growing in low-temperature environments. This scientific gap formed the basis of the present manuscript and explains the rationale for the introduction of cold-tolerant PSB in competitive agronomic practices, including the mechanism of solubilization/mineralization, release of biosensor active biomolecules, molecular engineering of PSB for increasing both P solubilizing/mineralizing efficiency, and host range. The impact of extreme cold on the physiological activities of plants and how plants overcome such stresses is discussed briefly. It is time to enlarge the prospects of psychrophilic/psychrotolerant phosphate biofertilizers and take advantage of their precious, fundamental, and economical but enormous plant growth augmenting potential to ameliorate stress and facilitate crop production to satisfy the food demands of frighteningly growing human populations. The production and application of cold-tolerant P-biofertilizers will recuperate sustainable agriculture in cold adaptive agrosystems.

New Insight into Bacterial Interaction with the Matrix of Plant-Based Fermented Foods

Microorganisms have been harnessed to process raw plants into fermented foods. The adaptation to a variety of plant environments has resulted in a nearly inseparable association between the bacterial species and the plant with a characteristic chemical profile. Lactic acid bacteria, which are known for their ability to adapt to nutrient-rich niches, have altered their genomes to dominate specific habitats through gene loss or gain. Molecular biology approaches provide a deep insight into the evolutionary process in many bacteria and their adaptation to colonize the plant matrix. Knowledge of the adaptive characteristics of microorganisms facilitates an efficient use thereof in fermentation to achieve desired final product properties. With their ability to acidify the environment and degrade plant compounds enzymatically, bacteria can modify the textural and organoleptic properties of the product and increase the bioavailability of plant matrix components. This article describes selected microorganisms and their competitive survival and adaptation in fermented fruit and vegetable environments. Beneficial changes in the plant matrix caused by microbial activity and their beneficial potential for human health are discussed as well.

Fermentation Strategies to Improve Soil Bio-Inoculant Production and Quality

The application of plant beneficial microorganisms has been widely accepted as an efficient alternative to chemical fertilizers and pesticides. Isolation and selection of efficient microorganisms, their characterization and testing in soil-plant systems are well studied. However, the production stage and formulation of the final products are not in the focus of the research, which affects the achievement of stable and consistent results in the field. Recent analysis of the field of plant beneficial microorganisms suggests a more integrated view on soil inoculants with a special emphasis on the inoculant production process, including fermentation, formulation, processes, and additives. This mini-review describes the different groups of fermentation processes and their characteristics, bearing in mind different factors, both nutritional and operational, which affect the biomass/spores yield and microbial metabolite activity. The characteristics of the final products of fermentation process optimization strategies determine further steps of development of the microbial inoculants. Submerged liquid and solid-state fermentation processes, fed-batch operations, immobilized cell systems, and production of arbuscular mycorrhiza are presented and their advantages and disadvantages are discussed. Recommendations for further development of the fermentation strategies for biofertilizer production are also considered.

High quality draft genome sequence of the type strain of Pseudomonas lutea OK2(T), a phosphate-solubilizing rhizospheric bacterium

Pseudomonas lutea OK2(T) (=LMG 21974(T), CECT 5822(T)) is the type strain of the species and was isolated from the rhizosphere of grass growing in Spain in 2003 based on its phosphate-solubilizing capacity. In order to identify the functional significance of phosphate solubilization in Pseudomonas Plant growth promoting rhizobacteria, we describe here the phenotypic characteristics of strain OK2(T) along with its high-quality draft genome sequence, its annotation, and analysis. The genome is comprised of 5,647,497 bp with 60.15 % G + C content. The sequence includes 4,846 protein-coding genes and 95 RNA genes.

Potential application of glycerol in the production of plant beneficial microorganisms

This review highlights the importance of research for development of biofertilizer and biocontrol products based on the use of glycerol for further process scale-up to industrial microbiology. Glycerol can be used successfully in all stages of production of plant beneficial microorganisms. It serves as an excellent substrate in both submerged and solid-state fermentation processes with free and immobilized microbial cells. Glycerol is also one of the most attractive formulation agents that ensures high cell density and viability including in harsh environmental conditions. Future research is discussed to make this inexpensive material a base for industrial production of plant beneficial microorganisms.

Enzymatic characterization of microbial isolates from lignocellulose waste composting: chronological evolution

Successful composting is dependent upon microbial performance. An interdependent relationship is established between environmental and nutritional properties that rule the process and characteristics of the dominant microbial communities. To reach a better understanding of this relationship, the dynamics of major metabolic activities associated with cultivable isolates according to composting phases were evaluated. Ammonification (72.04%), amylolysis (35.65%), hemicellulolyis (30.75%), and proteolysis (33.61%) were the more frequent activities among isolates, with mesophilic bacteria and fungi as the prevalent microbial communities. Bacteria were mainly responsible for starch hydrolysis, while a higher percentage of hemicellulolytic and proteolytic isolates were ascribable to fungi. Composting seems to exert a functional selective effect on microbial communities by promoting the presence of specific metabolically dominant groups at each stage of the process. Moreover, the application of conglomerate analysis led to the statement of a clear correlation between the chronology of the process and characteristics of the associated microbiota. According to metabolic capabilities of the isolates and their density, three clear clusters were obtained corresponding to the start of the process, including the first thermophilic peak, the rest of the bio-oxidative stage, and the maturation phase.

Microbial inoculants and organic amendment improves plant establishment and soil rehabilitation under semiarid conditions

The re-establishment of autochthonous shrub species is an essential strategy for recovering degraded soils under semiarid Mediterranean conditions. A field assay was carried out to determine the combined effects of the inoculation with native rhizobacteria (Bacillus megaterium, Enterobacter sp, Bacillus thuringiensis and Bacillus sp) and the addition of composted sugar beet (SB) residue on physicochemical soil properties and Lavandula dentata L. establishment. One year after planting, Bacillus sp. and B. megaterium + SB were the most effective treatments for increasing shoot dry biomass (by 5-fold with respect to control) and Enterobacter sp + SB was the most effective treatments for increasing dry root biomass. All the treatments evaluated significantly increased the foliar nutrient content (NPK) compared to control values (except B. thuringiensis + SB). The organic amendment had significantly increased available phosphorus content in rhizosphere soil by 29% respect to the control. Enterobacter sp combined with sugar beet residue improved total N content in soil (by 46% respect to the control) as well as microbiological and biochemical properties. The selection of the most efficient rhizobacteria strains and their combined effect with organic residue seems to be a critical point that drives the effectiveness of using these biotechnological tools for the revegetation and rehabilitation of degraded soils under semiarid conditions.

Coupled pot and lysimeter experiments assessing plant performance in microbially assisted phytoremediation

We performed an experiment at pot scale to assess the effect of plant growth-promoting bacteria (PGPB) on the development of five plant species grown on a tailing dam substrate. None of the species even germinated on inoculated unamended tailing material, prompting use of compost amendment. The effect of inoculation on the amended material was to increase soil respiration, and promote elements immobilisation at plant root surface. This was associated with a decrease in the concentrations of elements in the leaching water and an increase of plant biomass, statistically significant in the case of two species: Agrostis capillaris and Festuca rubra. The experiment was repeated at lysimeter scale with the species showing the best development at pot scale, A. capillaris, and the significant total biomass increase as a result of inoculation was confirmed. The patterns of element distribution in plants also changed (the concentrations of metals in the roots of A. capillaris and F. rubra significantly decreased in inoculated treatments, while phosphorus concentration significantly increased in roots of A. capillaris in inoculated treatment at lysimeter scale). Measured variables for plant oxidative stress did not change after inoculations. There were differences of A. capillaris plant-soil system response between experimental scales as a result of different substrate column structure and plant age at the sampling moment. Soil respiration was significantly larger at lysimeter scale than at pot scale. Leachate concentrations of As, Mn and Ni had significantly larger concentrations at lysimeter scale than at pot scale, while Zn concentrations were significantly smaller. Concentrations of several metals were significantly smaller in A. capillaris at lysimeter scale than at pot scale. From an applied perspective, a system A. capillaris-compost-PGPB selected from the rhizosphere of the tailing dam native plants can be an option for the phytostabilisation of tailing dams. Results should be confirmed by investigation at field plot scale.

Inhibition of Aspergillus niger phosphate solubilization by fluoride released from rock phosphate

The simultaneous release of various chemical elements with inhibitory potential for phosphate solubilization from rock phosphate (RP) was studied in this work. Al, B, Ba, Ca, F, Fe, Mn, Mo, Na, Ni, Pb, Rb, Si, Sr, V, Zn, and Zr were released concomitantly with P during the solubilization of Araxá RP (Brazil), but only F showed inhibitory effects on the process at the concentrations detected in the growth medium. Besides P solubilization, fluoride decreased fungal growth, citric acid production, and medium acidification by Aspergillus niger. At the maximum concentration found during Araxá RP solubilization (22.9 mg F(-) per liter), fluoride decreased P solubilization by 55%. These findings show that fluoride negatively affects RP solubilization by A. niger through its inhibitory action on the fungal metabolism. Given that fluoride is a common component of RPs, the data presented here suggest that most of the microbial RP solubilization systems studied so far were probably operated under suboptimal conditions.

Coexpression of the pyrroloquinoline quinone and glucose dehydrogenase genes from Serratia marcescens CTM 50650 conferred high mineral phosphate-solubilizing ability to Escherichia coli

The genes gdh and pqqABCDE encoding glucose dehydrogenase and its pyrroloquinoline quinone cofactor were cloned from the mineral phosphate-solubilizing (MPS) bacterium Serratia marcescens CTM 50650. We investigated, for the first time, the impact of their coexpression in Escherichia coli on MPS ability. The production of recombinant PQQGDH conferred high MPS activity to the engineered E. coli. In fact, the amounts of soluble phosphorus (P) produced from tricalcium phosphate, hydroxyapatite, and Gafsa rock phosphate (GRP) were 574, 426, and 217 mg/L, respectively. In an attempt to increase the soluble P concentration, the E. coli strain coexpressing the gdh and pqqABCDE genes was immobilized in agar, calcium alginate, and k-carrageenan and was then further applied in a repeated batch (six batches) fermentation process to solubilize GRP. Compared to other encapsulated systems, alginate cell beads were noted to yield the highest concentration of soluble P, which attained 300 mg/L/batch. MPS efficiency was maximal in the presence of 5 and 40 g/L of GRP and glucose, respectively.

Biochar of animal origin: a sustainable solution to the global problem of high-grade rock phosphate scarcity?

Phosphorus (P) is an essential element for all living organisms. However, in soil-plant systems, this nutrient is the most limiting, leading to frequent applications of soluble P fertilisers. Their excessive use provokes alterations in the natural P cycle, soil biodiversity and ecological equilibrium and is the main reason for the eutrophication of water, with consequences on food safety. Biotechnology offers a number of sustainable solutions that can mitigate these problems by using various waste materials as a source of P and, on the other hand, their solubilisation by selected micro-organisms. This review present results on the solubilisation of animal bone char with high phosphate content by micro-organisms to produce organic acids such as lactic acid, citric acid and itaconic acid. All experiments were performed under conditions of liquid submerged and solid state fermentation processes. Freely suspended and immobilised cells of the corresponding microbial cultures were employed using substrates characterised by low cost and abundance. Other alternative technologies are discussed as well in order to stimulate further studies in this field, bearing in mind the progressive increase in P fertiliser prices based on high global P consumption and the scarcity of rock phosphate reserves.

Technologies for beneficial microorganisms inocula used as biofertilizers

The increasing need for environmentaly friendly agricultural practices is driving the use of fertilizers based on beneficial microorganisms. The latter belong to a wide array of genera, classes, and phyla, ranging from bacteria to yeasts and fungi, which can support plant nutrition with different mechanisms. Moreover, studies on the interactions between plant, soil, and the different microorganisms are shedding light on their interrelationships thus providing new possible ways to exploit them for agricultural purposes. However, even though the inoculation of plants with these microorganisms is a well-known practice, the formulation of inocula with a reliable and consistent effect under field conditions is still a bottleneck for their wider use. The choice of the technology for inocula production and of the carrier for the formulation is key to their successful application. This paper focuses on how inoculation issues can be approached to improve the performance of beneficial microorganisms used as a tool for enhancing plant growth and yield.