Alginate beads as a storage, delivery and containment system for genetically modified PCB degrader and PCB biosensor derivatives of Pseudomonas fluorescens F113

Microbial bioformulation: a microbial assisted biostimulating fertilization technique for sustainable agriculture

Addressing the pressing issues of increased food demand, declining crop productivity under varying agroclimatic conditions, and the deteriorating soil health resulting from the overuse of agricultural chemicals, requires innovative and effective strategies for the present era. Microbial bioformulation technology is a revolutionary, and eco-friendly alternative to agrochemicals that paves the way for sustainable agriculture. This technology harnesses the power of potential microbial strains and their cell-free filtrate possessing specific properties, such as phosphorus, potassium, and zinc solubilization, nitrogen fixation, siderophore production, and pathogen protection. The application of microbial bioformulations offers several remarkable advantages, including its sustainable nature, plant probiotic properties, and long-term viability, positioning it as a promising technology for the future of agriculture. To maintain the survival and viability of microbial strains, diverse carrier materials are employed to provide essential nourishment and support. Various carrier materials with their unique pros and cons are available, and choosing the most appropriate one is a key consideration, as it substantially extends the shelf life of microbial cells and maintains the overall quality of the bioinoculants. An exemplary modern bioformulation technology involves immobilizing microbial cells and utilizing cell-free filters to preserve the efficacy of bioinoculants, showcasing cutting-edge progress in this field. Moreover, the effective delivery of bioformulations in agricultural fields is another critical aspect to improve their overall efficiency. Proper and suitable application of microbial formulations is essential to boost soil fertility, preserve the soil's microbial ecology, enhance soil nutrition, and support crop physiological and biochemical processes, leading to increased yields in a sustainable manner while reducing reliance on expensive and toxic agrochemicals. This manuscript centers on exploring microbial bioformulations and their carrier materials, providing insights into the selection criteria, the development process of bioformulations, precautions, and best practices for various agricultural lands. The potential of bioformulations in promoting plant growth and defense against pathogens and diseases, while addressing biosafety concerns, is also a focal point of this study.

Engineered Whole-Cell-Based Biosensors: Sensing Environmental Heavy Metal Pollutants in Water-a Review

The frequent exposure and accumulation of heavy metals in organisms cause serious health issues affecting a range of organs such as the brain, liver, and reproductive organs in adults, infants, and children. Several parts of the world have high levels of heavy metals affecting millions of people, costing millions of dollars for improving the potability of water and medical treatment of the affected. Hence, water quality assessment is required to monitor the degree of heavy metal contamination in potable water. In nature, organisms respond to various environmental pollutants such as heavy metals, allowing their survival in a diverse environmental niche. With the advent of recombinant DNA technology, it is now possible to manipulate these natural bioreporters into controlled systems which either turn on or off gene expression or activity of enzymes in the presence of specific heavy metals (compound-specific biosensors) otherwise termed as whole-cell biosensors (WCBs). WCBs provide an upper hand compared to other immunosensors, enzyme-based sensors, and DNA-based sensors since microbes can be relatively easily manipulated, scaled up with relative ease, and can detect only the bioavailable heavy metals. In this review, we summarize the current knowledge of the various mechanisms of toxicity elicited by various heavy metals, thence emphasizing the need to develop heavy metal sensing platforms. Following this, the biosensor-based platforms including WCBs for detecting heavy metals developed thus far have been briefly elaborated upon, emphasizing the challenges and solutions associated with WCBs.

Leveraging Pseudomonas Stress Response Mechanisms for Industrial Applications

Members of the genus Pseudomonas are metabolically versatile and capable of adapting to a wide variety of environments. Stress physiology of Pseudomonas strains has been extensively studied because of their biotechnological potential in agriculture as well as their medical importance with regards to pathogenicity and antibiotic resistance. This versatility and scientific relevance led to a substantial amount of information regarding the stress response of a diverse set of species such as Pseudomonas chlororaphis, P. fluorescens, P. putida, P. aeruginosa, and P. syringae. In this review, environmental and industrial stressors including desiccation, heat, and cold stress, are cataloged along with their corresponding mechanisms of survival in Pseudomonas. Mechanisms of survival are grouped by the type of inducing stress with a focus on adaptations such as synthesis of protective substances, biofilm formation, entering a non-culturable state, enlisting chaperones, transcription and translation regulation, and altering membrane composition. The strategies Pseudomonas strains utilize for survival can be leveraged during the development of beneficial strains to increase viability and product efficacy.

Immobilization of Bradyrhizobium and Azospirillum in alginate matrix for long time of storage maintains cell viability and interaction with peanut

Immobilizarion of PGPR for agricultural applications aims to provide temporary physical protection from stressful environmental conditions and the gradual release of cells for successful root colonization, release the cells gradually. In this work, we immobilized Bradyrhizobium sp. SEMIA6144 or Azospirillum brasilense Az39 cells in 2% alginate beads prepared by ionic gelation process, and then stored up to 12 months at 4 °C. Alginate matrix showed interaction with the immobilized bacteria (FTIR), allowed a constant release of cells, and improved their viability and capability to interact with Arachis hypogaea. Cell number into beads reached 10⁷ CFU.bead^-1; however, viability decreased from 4 months of storage for Az39, while it was maintained up to 12 months for SEMIA6144, showing a low metabolic activity measured by the MTT assay. Adhesion of SEMIA6144 and Az39 from new beads to peanut root was 11.5% and 16%, respectively, higher than non-immobilized bacteria. Peanut inoculation with 12 months storage SEMIA6144 beads significantly increased root length and biomass at 30 days of growth, and under restrictive water condition (RWC), nodulation and total plant N content increased compared with liquid inoculation. Our results demonstrate that immobilization of SEMIA6144 and Az39 in alginate matrix is a potential alternative to enhance peanut growth even under RWC. KEY POINTS: • Alginate encapsulation enhances viability of SEMIA6144 or Az39 under storage at 4 °C for 1 year. • Alginate beads 2% ensure the gradual release of the microorganisms. • Cells from beads stored for long periods present chemotaxis and adhesion to peanut root. • Peanut inoculation with 1-year-old SEMIA6144 beads improves nodulation and growth in RWC.

Formulation of Microbial Inoculants by Encapsulation in Natural Polysaccharides: Focus on Beneficial Properties of Carrier Additives and Derivatives

In the last 10-15 years, the wide application of bioformulated plant beneficial microorganisms is accepted as an effective alternative of chemical agro-products. Two main problems can be distinguished in their production and application: (a) economical competiveness based on the overall up-stream and down-stream operational costs, and (b) development of commercial products with a high soil-plant colonization potential in controlled conditions but not able to effectively mobilize soil nutrients and/or combat plant pathogens in the field. To solve the above problems, microbe-based formulations produced by immobilization methods are gaining attention as they demonstrate a large number of advantages compared to other solid and liquid formulations. This mini-review summarizes the knowledge of additional compounds that form part of the bioformulations. The additives can exert economical, price-decreasing effects as bulking agents or direct effects improving microbial survival during storage and after introduction into soil with simultaneous beneficial effects on soil and plants. In some studies, combinations of additives are used with a complex impact, which improves the overall characteristics of the final products. Special attention is paid to polysaccharide carriers and their derivates, which play stimulatory role on plants but are less studied. The mini-review also focuses on the potential difficulty in evaluating the effects of complex bio-formulations.

Synthetic Biology Enables Programmable Cell-Based Biosensors

Cell-based biosensors offer cheap, portable and simple methods of detecting molecules of interest but have yet to be truly adopted commercially. Issues with their performance and specificity initially slowed the development of cell-based biosensors. With the development of rational approaches to tune response curves, the performance of biosensors has rapidly improved and there are now many biosensors capable of sensing with the required performance. This has stimulated an increased interest in biosensors and their commercial potential. However the reliability, long term stability and biosecurity of these sensors are still barriers to commercial application and public acceptance. Research into overcoming these issues remains active. Here we present the state-of-the-art tools offered by synthetic biology to allow construction of cell-based biosensors with customisable performance to meet the real world requirements in terms of sensitivity and dynamic range and discuss the research progress to overcome the challenges in terms of the sensor stability and biosecurity fears.

Remediation of Organically Contaminated Soil Through the Combination of Assisted Phytoremediation and Bioaugmentation

Here, we aimed to bioremediate organically contaminated soil with Brassica napus and a bacterial consortium. The bioaugmentation consortium consisted of four endophyte strains that showed plant growth-promoting traits (three Pseudomonas and one Microbacterium) plus three strains with the capacity to degrade organic compounds (Burkholderia xenovorans LB400, Paenibacillus sp. and Lysinibacillus sp.). The organically contaminated soil was supplemented with rhamnolipid biosurfactant and sodium dodecyl benzenesulfonate to increase the degradability of the sorbed contaminants. Soils were treated with organic amendments (composted horse manure vs. dried cow slurry) to promote plant growth and stimulate soil microbial activity. Apart from quantification of the expected decrease in contaminant concentrations (total petroleum hydrocarbons, polycyclic aromatic hydrocarbons), the effectiveness of our approach was assessed in terms of the recovery of soil health, as reflected by the values of different microbial indicators of soil health. Although the applied treatments did not achieve a significant decrease in contaminant concentrations, a significant improvement of soil health was observed in our amended soils (especially in soils amended with dried cow slurry), pointing out a not-so-uncommon situation in which remediation efforts fail from the point of view of the reduction in contaminant concentrations while succeeding to recover soil health.

Application of Endophytic Pseudomonas fluorescens and a Bacterial Consortium to Brassica napus Can Increase Plant Height and Biomass under Greenhouse and Field Conditions

Plant associated bacteria with plant growth promotion (PGP) properties have been proposed for use as environmentally friendly biofertilizers for sustainable agriculture; however, analysis of their efficacy in the field is often limited. In this study, greenhouse and field trials were carried out using individual endophytic Pseudomonas fluorescens strains, the well characterized rhizospheric P. fluorescens F113 and an endophytic microbial consortium of 10 different strains. These bacteria had been previously characterized with respect to their PGP properties in vitro and had been shown to harbor a range of traits associated with PGP including siderophore production, 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity, and inorganic phosphate solubilization. In greenhouse experiments individual strains tagged with gfp and Km^r were applied to Brassica napus as a seed coat and were shown to effectively colonize the rhizosphere and root of B. napus and in addition they demonstrated a significant increase in plant biomass compared with the non-inoculated control. In the field experiment, the bacteria (individual and consortium) were spray inoculated to winter oilseed rape B. napus var. Compass which was grown under standard North Western European agronomic conditions. Analysis of the data provides evidence that the application of the live bacterial biofertilizers can enhance aspects of crop development in B. napus at field scale. The field data demonstrated statistically significant increases in crop height, stem/leaf, and pod biomass, particularly, in the case of the consortium inoculated treatment. However, although seed and oil yield were increased in the field in response to inoculation, these data were not statistically significant under the experimental conditions tested. Future field trials will investigate the effectiveness of the inoculants under different agronomic conditions.

Alginate immobilized enrichment culture for atrazine degradation in soil and water system

An atrazine degrading enrichment culture, a consortium of bacteria of genus Bacillus along with Pseudomonas and Burkholderia, was immobilized in sodium alginate and was used to study atrazine degradation in mineral salts medium (MSM), soil and wastewater effluent. Sodium alginate immobilized consortium, when stored at room temperature (24 ± 5°C), was effective in degrading atrazine in MSM up to 90 days of storage. The survival of bacteria in alginate beads, based on colony formation unit (CFU) counts, suggested survival up to 90 days and population counts decreased to 1/5^th on 120 days. Comparison of atrazine degrading ability of the freely suspended enrichment culture and immobilized culture suggested that the immobilized culture took longer time for complete degradation of atrazine as a lag phase of 2 days was observed in the MSM inoculated with alginate immobilized culture. The free cells resulted in complete degradation of atrazine within 6 days, while immobilized cells took 10 days for 100% atrazine degradation. Further, immobilized cultures were able to degrade atrazine in soil and wastewater effluent. Alginate beads were stable and effective in degrading atrazine till 3rd transfer and disintegrated thereafter. The study suggested that immobilized enrichment culture, due to its better storage and application, can be used to degrade atrazine in soil water system.

Plant growth promotion induced by phosphate solubilizing endophytic Pseudomonas isolates

The use of plant growth promoting bacterial inoculants as live microbial biofertilizers provides a promising alternative to chemical fertilizers and pesticides. Inorganic phosphate solubilization is one of the major mechanisms of plant growth promotion by plant associated bacteria. This involves bacteria releasing organic acids into the soil which solubilize the phosphate complexes converting them into ortho-phosphate which is available for plant up-take and utilization. The study presented here describes the ability of endophytic bacteria to produce gluconic acid (GA), solubilize insoluble phosphate, and stimulate the growth of Pisum sativum L. plants. This study also describes the genetic systems within three of these endophyte strains thought to be responsible for their effective phosphate solubilizing abilities. The results showed that many of the endophytic strains produced GA (14–169 mM) and have moderate to high phosphate solubilization capacities (~400–1300 mg L⁻¹). When inoculated into P. sativum L. plants grown in soil under soluble phosphate limiting conditions, the endophytes that produced medium-high levels of GA displayed beneficial plant growth promotion effects.

Ecopiling: a combined phytoremediation and passive biopiling system for remediating hydrocarbon impacted soils at field scale

Biopiling is an ex situ bioremediation technology that has been extensively used for remediating a wide range of petrochemical contaminants in soils. Biopiling involves the assembling of contaminated soils into piles and stimulating the biodegrading activity of microbial populations by creating near optimum growth conditions. Phytoremediation is another very successful bioremediation technique and involves the use of plants and their associated microbiomes to degrade, sequester or bio-accumulate pollutants from contaminated soil and water. The objective of this study was to investigate the effectiveness of a combined phytoremediation/biopiling system, termed Ecopiling, to remediate hydrocarbon impacted industrial soil. The large scale project was carried out on a sandy loam, petroleum impacted soil [1613 mg total petroleum hydrocarbons (TPHs) kg(-1) soil]. The contaminated soil was amended with chemical fertilizers, inoculated with TPH degrading bacterial consortia and then used to construct passive biopiles. Finally, a phyto-cap of perennial rye grass (Lolium perenne) and white clover (Trifolium repens) was sown on the soil surface to complete the Ecopile. Monitoring of important physico-chemical parameters was carried out at regular intervals throughout the trial. Two years after construction the TPH levels in the petroleum impacted Ecopiles were below detectable limits in all but one subsample (152 mg TPH kg(-1) soil). The Ecopile system is a multi-factorial bioremediation process involving bio-stimulation, bio-augmentation and phytoremediation. One of the key advantages to this system is the reduced costs of the remediation process, as once constructed, there is little additional cost in terms of labor and maintenance (although the longer process time may incur additional monitoring costs). The other major advantage is that many ecological functions are rapidly restored to the site and the process is esthetically pleasing.

Optimization of cultural conditions of Arthrobacter sp. Sphe3 for growth-associated chromate(VI) reduction in free and immobilized cell systems

The current study aimed to characterize Arthrobacter sp. Sphe3 ability to reduce Cr(VI) in suspended cell cultures as well as in immobilized form using Ca-alginate beads. Adaptation studies in the presence of 5 mg L(-1) Cr(VI) showed a significant increase in specific growth rate from 0.25 to 0.3 h(-1) and bioremoval percentage from 64% to 94% (p<0.05), whereas Arthrobacter sp. Sphe3 could tolerate up to 50 mg L(-1) Cr(VI). Optimization of culture conditions resulted in complete reduction of 45 mg L(-1) Cr(VI) at 30 °C, pH 8 and 10 g L(-1) of glucose. High glucose concentrations helped at reducing (80±2.4)% of initial 100 mg L(-1) Cr(VI), whereas the bacterial strain could tolerate 850 mg L(-1) Cr(VI). Cr(III) formation was first evidenced by the appearance of a green insoluble precipitate in the medium. Cell biomass was successfully immobilized in Ca-alginate beads that were evaluated for their stability. Cell release was sharply decreased when 4% Na-alginate was used under non-shaking conditions. Biotransformation efficiency was enhanced when 25-50 mg cells mL(-1) Na-alginate from the exponential growth phase were collected and co-encapsulated with either 1% glucose and 0.5% (NH4)2SO4, or 1% LB medium. Immobilized biocatalyst could be reused up to 6 continuous cycles in the presence of 10 mg L(-1) Cr(VI), but its performance was lowered at higher metal concentrations comparing with free cells that significantly maintained their reducing ability up to 300 mg L(-1) Cr(VI).

Optimizing alginate beads for the immobilisation of Phaeodactylum tricornutum in estuarine waters

This study addresses the influence of calcium as hardening agent, on alginate gel bead stability and suitability for the growth of Phaeodactylum tricornutum Bohlin (Bacillariophyceae) in estuarine waters. Alginate beads produced with 1, 2, 4, 5 and 6% of CaCl2 solutions were investigated for stability and suitability for growth of P. tricornutum cells, under mean salinity 27, at 220 and 440 rpm stirring laboratory conditions, and in devices placed under in situ estuarine conditions. Gel stability and suitability for cell growth were evaluated through bead diameter, bead disruption, dissolution and loss of spherical shape, cell viability and specific growth rates. Beads gelled with 5% CaCl2 were found the most suitable to sustain gel stability and cell growth in the estuarine waters. These beads were surveyed during dredging operations in the Tagus estuary, both in situ and in estuarine water under laboratory conditions, showing significantly lowered growth rates possibly due to Mn, Co and As accumulated in the cells. Results confirmed that the monitoring tool presented is reliable and effective for the assessment of anthropogenic impacts.