Effect of immobilization of a bacterial consortium on diuron dissipation and community dynamics

Synergizing biotechnology and natural farming: pioneering agricultural sustainability through innovative interventions

The world has undergone a remarkable transformation from the era of famines to an age of global food production that caters to an exponentially growing population. This transformation has been made possible by significant agricultural revolutions, marked by the intensification of agriculture through the infusion of mechanical, industrial, and economic inputs. However, this rapid advancement in agriculture has also brought about the proliferation of agricultural inputs such as pesticides, fertilizers, and irrigation, which have given rise to long-term environmental crises. Over the past two decades, we have witnessed a concerning plateau in crop production, the loss of arable land, and dramatic shifts in climatic conditions. These challenges have underscored the urgent need to protect our global commons, particularly the environment, through a participatory approach that involves countries worldwide, regardless of their developmental status. To achieve the goal of sustainability in agriculture, it is imperative to adopt multidisciplinary approaches that integrate fields such as biology, engineering, chemistry, economics, and community development. One noteworthy initiative in this regard is Zero Budget Natural Farming, which highlights the significance of leveraging the synergistic effects of both plant and animal products to enhance crop establishment, build soil fertility, and promote the proliferation of beneficial microorganisms. The ultimate aim is to create self-sustainable agro-ecosystems. This review advocates for the incorporation of biotechnological tools in natural farming to expedite the dynamism of such systems in an eco-friendly manner. By harnessing the power of biotechnology, we can increase the productivity of agro-ecology and generate abundant supplies of food, feed, fiber, and nutraceuticals to meet the needs of our ever-expanding global population.

Paenibacillus sp. Strain OL15 Immobilized in Agar as a Potential Bioremediator for Waste Lubricating Oil-Contaminated Soils and Insights into Soil Bacterial Communities Affected by Inoculations of the Strain and Environmental Factors

Waste lubricating oil is a widespread common soil pollutant. In this study, the waste lubricating oil degraders were isolated from the oil-contaminated soil. The bacterial strains OL6, OL15, and OL8, which tolerated a high concentration (10%) of waste lubricating oil, presented the degradation efficiency values (measured in culture broth) of 15.6 ± 0.6%, 15.5 ± 1%, and 14.8 ± 1%, respectively, and belonged to the genera Enterobacter, Paenibacillus, and Klebsiella, respectively. To maintain long survival, immobilization of a promising bioremediator, Paenibacillus sp. strain OL15, in agar exhibited the significantly highest number of surviving cells at the end of a 30-day incubation period, as compared to those in alginate and free cells. Remarkably, after being introduced into the soil contaminated with 10% waste lubricating oil, the strain OL15 immobilized in agar conferred the highest degradation percentage up to 45 ± 3%. Due to its merit as a promising soil pollutant degrader, we investigated the effect of an introduction of the strain OL15 on the alterations of a bacterial community in the oil-contaminated soil environments using 16S rRNA amplicon sequencing. The result revealed that the Proteobacteria, Acidobacteriota, Firmicutes, and Actinobacteriota were predominant phyla. The introduction of the strain affected the soil bacterial community structures by increasing total bacterial diversity and richness. The proportions of the genera Pseudomonas, Vibrio, Herbaspirillum, Pseudoalteromonas, Massilia, Duganella, Bacillus, Gordonia, and Sulfurospirillum were altered in response to the strain establishment. Soil pH, EC, OM, total N, P, Mg, Fe, and Zn were the major factors influencing the bacterial community compositions in the oil-contaminated soils.

Effect of Pseudomonas putida-producing pyoverdine on copper uptake by Helianthus annuus cultivated on vineyard soils

Bioaugmentation-assisted phytoextraction was used to reduce the Cu load in vineyard soils. While performance is usually the endpoint of such studies, here we identified some mechanisms underlying Cu soil to plant transfer, particularly the role of siderophores in the extraction of Cu from the soil-bearing phases and its phytoavailability. Carbonated vs. non‑carbonated vineyard soils were cultivated with sunflower in rhizoboxes bioaugmented with Pseudomonas putida. gfp-Tagged P. putida was monitored in the soil and pyoverdine (Pvd), Cu, Fe, Mn, and Zn were measured in the soil solution. Trace elements (TE) were analysed in the roots and shoots. Plant growth and nutritional status were also measured. With bioaugmentation, the concentration of total Cu (vs. Cu²⁺) in the soil solution increased (decreased) by a factor of 1.6 to 2.6 (7 to 13) depending on the soil. The almost 1:1 relationship between the excess of Fe + Cu mobilized from the solid phase and the amount of Pvd in the soil solution in bioaugmented treatments suggests that Pvd mobilized Fe and Cu mainly by ligand-controlled dissolution via a 1:1 metal-Pvd complex. Bioaugmentation increased the Cu concentration by 17% in the shoots and by 93% in the roots, and by 30% to 60% the sunflower shoot biomass leading to an increase in the amount of Cu phytoextracted by up to 87%. The amount of Fe, Mn, Zn, and P also increased in the roots and shoots. Contrary to what was expected, carbonated soil did not increase the mobilization of TE. Our results showed that bioaugmentation increased phytoextraction, and its performance can be further improved by promoting the dissociation of Pvd-Cu complex in the solution at the soil-root interface.

Encapsulation of Azotobacter vinelandii ATCC 12837 in Alginate-Na Beads as a Tomato Seedling Inoculant

Encapsulation is an immobilization method characterized by restricting microbial cells to a delimited area while preserving their metabolic viability. This technique represents an alternative to improve the adaptive capacity of bacteria in the face of interactions with native microorganisms and environmental factors that limit their inoculation. This study aimed to evaluate the effect of Azotobacter vinelandii ATCC 12837 encapsulated in alginate-Na beads as an inoculant of tomato (Solanum Lycopersicum L) seedlings. Two inoculation treatments were carried out: liquid and encapsulated, and the control without microorganisms. Physiological variables, microbial viability, and the presence of A. vinelandii were determined by qPCR. Inoculation with A. vinelandii in liquid and encapsulated form favored seedling growth. Plants with the encapsulated inoculum significantly increased germination percentage (20%), stem diameter (38%), seedling height (34%), root length (69%), NO₃ concentration (41%), and Na (30%); compared to the control. Encapsulation of A. vinelandii in alginate-Na macrocapsules allowed its establishment in the rhizosphere and was corroborated by viable count and molecular methods. The viability of the bacteria was maintained for 28 days using both inoculation methods, and not detected in the control treatment.

Degradation of Diuron by a Bacterial Mixture and Shifts in the Bacterial Community During Bioremediation of Contaminated Soil

Diuron, a phenylurea herbicide, has been extensively applied in controlling a wide range of weeds in several crops. In the current study, a mixed culture of three bacterial strains, i.e., Bacillus subtilis DU1, Acinetobacter baumannii DU, and Pseudomonas sp. DUK, isolated from sugarcane soil, completely degraded diuron and 3,4-DCA in liquid media at 20 mg L^-1 within 48 h. During diuron degradation, a few metabolites (DCPMU, DCPU, and 3,4-DCA) were produced. Further determination of ring-cleavage pathways demonstrated that Acinetobacter baumannii DU and Pseudomonas fluorescens DUK degraded diuron and 3,4-DCA via ortho-cleavage. In contrast, Bacillus subtilis DU transformed these compounds via meta-cleavage pathways. Moreover, diuron caused a significant shift in the bacterial community in soil without diuron history. The augmentation of mountain soil with the isolated bacteria resulted in nearly three times higher degradation rate of diuron than the degradation by indigenous microorganisms. This study provides important information on in situ diuron bioremediation from contaminated sites by bioaugmentation with a mixed bacterial culture.

Co-culturing microbial consortia: approaches for applications in biomanufacturing and bioprocessing

The application of microbial co-cultures is now recognized in the fields of biotechnology, ecology, and medicine. Understanding the biological interactions that govern the association of microorganisms would shape the way in which artificial/synthetic co-cultures or consortia are developed. The ability to accurately predict and control cell-to-cell interactions fully would be a significant enabler in synthetic biology. Co-culturing method development holds the key to strategically engineer environments in which the co-cultured microorganism can be monitored. Various approaches have been employed which aim to emulate the natural environment and gain access to the untapped natural resources emerging from cross-talk between partners. Amongst these methods are the use of a communal liquid medium for growth, use of a solid-liquid interface, membrane separation, spatial separation, and use of microfluidics systems. Maximizing the information content of interactions monitored is one of the major challenges that needs to be addressed by these designs. This review critically evaluates the significance and drawbacks of the co-culturing approaches used to this day in biotechnological applications, relevant to biomanufacturing. It is recommended that experimental results for a co-cultured species should be validated with different co-culture approaches due to variations in interactions that could exist as a result of the culturing method selected.

Diuron degradation by bacteria from soil of sugarcane crops

The isolation of microorganisms from soil impacted by xenobiotic chemicals and exposing them in the laboratory to the contaminant can provide important information about their response to the contaminants. The purpose of this study was to isolate bacteria from soil with historical application of herbicides and to evaluate their potential to degrade diuron. The isolation media contained either glucose or diuron as carbon source. A total of 400 bacteria were isolated, with 68% being Gram-positive and 32% Gram-negative. Most isolates showed potential to degrade between 10 and 30% diuron after five days of cultivation; however Stenotrophomonas acidophila TD4.7 and Bacillus cereus TD4.31 were able to degrade 87% and 68%, respectively. The degradation of diuron resulted in the formation of the metabolites DCPMU, DCPU, DCA, 3,4-CAC, 4-CA, 4-CAC and aniline. Based on these results it was proposed that Pseudomonas aeruginosa TD2.3, Stenotrophomonas acidaminiphila TD4.7, B. cereus TD4.31 and Alcaligenes faecalis TG 4.48, act on 3,4-DCA and 4-CA by alkylation and dealkylation while Micrococcus luteus and Achromobacter sp follow dehalogenation directly to aniline. Growth on aniline as sole carbon source demonstrates the capacity of strains to open the aromatic ring. In conclusion, the results show that the role of microorganisms in the degradation of xenobiotics in the environment depends on their own metabolism and also on their synergistic interactions.

Immobilized and MgSO4 induced cost effective bacterial disintegration of waste activated sludge for effective anaerobic digestion

In this study, an attempt was made to disintegrate waste activated sludge (WAS) in a cost-effective way. During the first phase of this study, effective break down of extracellular polymeric substance (EPS) was performed by deflocculating WAS with 0.1 g/g SS of MgSO₄. Deflocculation rate was 92% with discharge rate of extractable EPS at 185 mg/L. In the second phase, effective bacterial cell disintegration was obtained at 36 h post treatment. Maximum solubilization of deflocculated sludge was approximately 21%, which was higher than that of flocculated sludge (14.2%) or the control (4.5%). Biodegradability studies were assessed through kinetic analysis by non-linear regression modeling. Results revealed that the deflocculated sludge had higher methane generation (at about 235.8 mL/gVs) compared to flocculated sludge (at 146.1 mL/gVs) or the control (at 34.8 mL/gVs). Cost assessment of the present work revealed that the net yield for each ton of the deflocculated sludge was about 32.99 USD.

Upgrading the hydrolytic potential of immobilized bacterial pretreatment to boost biogas production

In this study, surfactant dioctyl sodium sulphosuccinate (DOSS)-mediated immobilized bacterial pretreatment of waste activated sludge (WAS) was experimentally proved to be an efficient and economically feasible process for enhancing the biodegradability of WAS. The maximal floc disruption with negligible cell cleavage was achieved at surfactant dosage of 0.009 g/g SS. Results of the outcome of bacterial pretreatment of sludge biomass revealed that chemical oxygen demand (COD) solubilization for deflocculated (EPS removed-bacterially pretreated) sludge was 20 %, which was higher than that of flocculated (14 %) or control (5 %). The pretreatment was swift in deflocculated sludge with a rate constant of about 0.064 h^-1. Biochemical methane potential (BMP) assay resulted in significant methane yield at 0.24 gCOD/gCOD for deflocculated sludge. Economic assessment of the proposed method showed a net profit of about 57.39 USD/ton of sludge.

Actinobacteria: Current research and perspectives for bioremediation of pesticides and heavy metals

Actinobacteria exhibit cosmopolitan distribution since their members are widely distributed in aquatic and terrestrial ecosystems. In the environment they play relevant ecological roles including recycling of substances, degradation of complex polymers, and production of bioactive molecules. Biotechnological potential of actinobacteria in the environment was demonstrated by their ability to remove organic and inorganic pollutants. This ability is the reason why actinobacteria have received special attention as candidates for bioremediation, which has gained importance because of the widespread release of contaminants into the environment. Among organic contaminants, pesticides are widely used for pest control, although the negative impact of these chemicals in the environmental balance is increasingly becoming apparent. Similarly, the extensive application of heavy metals in industrial processes lead to highly contaminated areas worldwide. Several studies focused in the use of actinobacteria for cleaning up the environment were performed in the last 15 years. Strategies such as bioaugmentation, biostimulation, cell immobilization, production of biosurfactants, design of defined mixed cultures and the use of plant-microbe systems were developed to enhance the capabilities of actinobacteria in bioremediation. In this review, we compiled and discussed works focused in the study of different bioremediation strategies using actinobacteria and how they contributed to the improvement of the already existing strategies. In addition, we discuss the importance of omic studies to elucidate mechanisms and regulations that bacteria use to cope with pollutant toxicity, since they are still little known in actinobacteria. A brief account of sources and harmful effects of pesticides and heavy metals is also given.

Immobilization of Multi-biocatalysts in Alginate Beads for Cofactor Regeneration and Improved Reusability

We have recently developed a simple, reusable and coupled whole-cell biocatalytic system with the capability of cofactor regeneration and biocatalyst immobilization for improved production yield and sustained synthesis. Described herewith is the experimental procedure for the development of such a system consisting of two E. coli strains that express functionally complementary enzymes. Together, these two enzymes can function co-operatively to mediate the regeneration of expensive cofactors for improving the product yield of the bioreaction. In addition, the method of synthesizing an immobilized form of the coupled biocatalytic system by encapsulation of whole cells in calcium alginate beads is reported. As an example, we present the improved biosynthesis of L-xylulose from L-arabinitol by coupling E. coli cells expressing the enzymes L-arabinitol dehydrogenase or NADH oxidase. Under optimal conditions and using an initial concentration of 150 mM L-arabinitol, the maximal L-xylulose yield reached 96%, which is higher than those reported in the literature. The immobilized form of the coupled whole-cell biocatalysts demonstrated good operational stability, maintaining 65% of the yield obtained in the first cycle after 7 cycles of successive re-use, while the free cell system almost completely lost the catalytic activity. Therefore, the methods reported here provides two strategies that could help improve the industrial production of L-xylulose, as well as other value-added compounds requiring the use of cofactors in general.

A TiO2modified abiotic–biotic process for the degradation of the azo dye methyl orange

Methyl orange was degraded by a TiO₂modified abiotic–biotic process involving synergetic mechanisms of adsorption, biodegradation, dye sensitization and LMCT.

Assisted attenuation of a soil contaminated by diuron using hydroxypropyl-β-cyclodextrin and organic amendments

Diuron desorption and mineralisation were studied on an amended and artificially contaminated soil. The amendments used comprised two different composted organic residues i.e., sewage sludge (SS) mixed with pruning wastes, and urban solid residues (USR), and two different solutions (with inorganic salts as the micronutrients and hydroxypropyl-β-cyclodextrin (HPBCD)). After applying micronutrients to activate the soil flora, 15.5% mineralisation could be reached after 150 days, indicating that the soil has a potential capacity to mineralise the herbicide through biostimulation-assisted attenuation. Diuron mineralisation was also improved when HPBCD solutions were applied. Indeed, the extent of herbicide mineralisation reached 29.7% with this application. Moreover, both the lag phase and the half-life time (DT50) were reduced to 33 and 1,778 days, respectively, relative to the application of just micronutrients (i.e., 39 and 6297 days, respectively). Organic amendments were also applied (i.e., USR and SS) on the contaminated soil: it was found that the diuron mineralisation rate was improved as the amendment concentration increased. The joint application of all treatments investigated at the best conditions tested was conducted to obtain the best diuron mineralisation results. The micronutrient amendment plus 4% USR or SS amendment plus HPBCD solution (10-fold diuron initially spiked) caused an extent of diuron mineralisation 33.2 or 46.5%, respectively.

Lindane removal by pure and mixed cultures of immobilized actinobacteria

Lindane (γ-HCH) is an organochlorine insecticide that has been widely used in developing countries. It is known to persist in the environment and can cause serious health problems. One of the strategies adopted to remove lindane from the environment is bioremediation using microorganisms. Immobilized cells present advantages over free suspended cells, like their high degradation efficiency and protection against toxins. The aims of this work were: (1) To evaluate the ability of Streptomyces strains immobilized in four different matrices to remove lindane, (2) To select the support with optimum lindane removal by pure cultures, (3) To assay the selected support with consortia and (4) To evaluate the reusability of the immobilized cells. Four Streptomyces sp. strains had previously shown their ability to grow in the presence of lindane. Lindane removal by microorganisms immobilized was significantly higher than in free cells. Specifically immobilized cells in cloth sachets showed an improvement of around 25% in lindane removal compared to the abiotic control. Three strains showed significantly higher microbial growth when they were entrapped in silicone tubes. Strains immobilized in PVA-alginate demonstrated lowest growth. Mixed cultures immobilized inside cloth sachets showed no significant enhancement compared to pure cultures, reaching a maximum removal of 81% after 96 h for consortium I, consisting of the four immobilized strains together. Nevertheless, the cells could be reused for two additional cycles of 96 h each, obtaining a maximum removal efficiency of 71.5% when each of the four strains was immobilized in a separate bag (consortium III).

Biotransformation and biomonitoring of phenylurea herbicide diuron

A Gram-positive, Micrococcus sp. strain PS-1 isolated from diuron storage site was studied for its capability of biotransformation of phenylurea herbicide diuron to a secondary metabolite, 1-(3,4-dichlorophenyl)urea (DCPU) for bioconjugation and antibody development applications. The metabolite formed associated with profound changes in bacterial cell morphology demonstrated increase in the degradation kinetics of diuron in presence of small quantity of a surfactant. The synthesized metabolite identified by chromatographic and mass spectrometry techniques was conjugated with carrier protein, and used as an immunogen for antibodies production. The generated antibody was highly specific, demonstrating excellent sensitivity against diuron. The antibody was used as receptor molecules in standard fluorescence immunoassay (FIA) format showing detection limit of 0.01 ng/mL in the optimum working concentration range of diuron with good signal precision (∼2%). The study presented first time the degradation pathway of herbicide by specific microorganism to synthesize hapten for bioconjugation and immunoassay development.

Biodegradation in a partially saturated sand matrix: compounding effects of water content, bacterial spatial distribution, and motility

Bacterial pesticide degraders are generally heterogeneously distributed in soils, leaving soil volumes devoid of degradation potential. This is expected to have an impact on degradation rates because the degradation of pollutant molecules in such zones will be contingent either on degraders colonizing these zones or on pollutant mass transfer to neighboring zones containing degraders. In a model system, we quantified the role exerted by water on mineralization rate in the context of a heterogeneously distributed degradation potential. Alginate beads colonized by Pseudomonas putida KT2440 were inserted at prescribed locations in sand microcosms so that the initial spatial distribution of the mineralization potential was controlled. The mineralization rate was strongly affected by the matric potential (decreasing rate with decreasing matric potential) and by the initial distribution of the degraders (more aggregated distributions being associated with lower rates). The mineralization was diffusion-limited, as confirmed with a mathematical model. In wet conditions, extensive cell dispersal was observed for the flagellated wild type and, albeit to a lesser extent, for a nonflagellated mutant, partially relieving the diffusion limitation. Dry conditions, however, sustained low mineralization rates through the combined effects of low pollutant diffusivity and limited degrader dispersal.