Biofilms and nanoparticles: applications in agriculture

Emerging models to study competitive interactions within bacterial communities

Within both abiotic and host environments, bacteria typically exist as diverse, multispecies communities and have crucial roles in human health, agriculture, and industry. In these communities, bacteria compete for resources, and these competitive interactions can shape the overall population structure and community function. Studying bacterial community dynamics requires experimental model systems that capture the different interaction networks between bacteria and their surroundings. We examine the recent literature advancing such systems, including (i) in silico models establishing the theoretical basis for how cell-to-cell interactions can influence population level dynamics, (ii) in vitro models characterizing specific interbacterial interactions, (iii) organ-on-a-chip models revealing the physiologically relevant parameters, such as spatial structure and mechanical forces, that bacteria encounter within a host, and (iv) in vivo plant and animal models connecting the host responses to interbacterial interactions. Each of these systems has greatly contributed to our understanding of bacterial community dynamics and can be used synergistically to understand how bacterial competition influences population architecture.

Growth period and variety together drive the succession of phyllosphere microbial communities of grapevine

Phyllosphere microbes play a crucial role in plant health and productivity. However, the influence of abiotic and biotic factors on these communities is poorly understood. Here, we used amplicon sequencing to investigate the microbiome variations across eight grape cultivars and three distinct leaf ages. The diversity and richness of phyllosphere microbiomes were significantly affected by cultivars and leaf age. Young leaves of most grape cultivars had a higher diversity. Beta-diversity analyses revealed notable differences in microbial communities across leaf ages, with bacterial communities varying substantially between cultivars. The main bacterial genera included Staphylococcus, Exiguobacterium, Acinetobacter, Enterococcus, and Erwinia; the principal fungal genera were Cladosporium, Moesziomyces, Alternaria, Didymella, and Coprinellus across all samples. LEfSe analysis revealed significant differences in bacterial and fungal biomarkers at different leaf ages, with no biomarkers identified among different cultivars. Fungal biomarkers were more abundant than bacterial at three leaf ages, and older leaves had more fungal biomarkers. Notably, beneficial microbial taxa with biocontrol potential were present on the phyllosphere at 45 d, whereas certain fungal groups associated with increased disease risk were first detected at 100 d. The bacterial network was more complex than the fungal network, and young leaves had a more complex network in most cultivars. Our study elucidated the dynamics of early grape phyllosphere microbes, providing valuable insights for early detection and prediction of grape diseases and a foundation for leveraging the grape leaf microbiome for agricultural purposes.

Enterococcus mundtii A2 biofilm and its anti-adherence potential against pathogenic microorganisms on stainless steel 316L

Pathogenic bacterial biofilms present significant challenges, particularly in food safety and material deterioration. Therefore, using Enterococcus mundtii A2, known for its antagonistic activity against pathogen adhesion, could serve as a novel strategy to reduce pathogenic colonization within the food sector. This study aimed to investigate the biofilm-forming ability of E. mundtii A2, isolated from camel milk, on two widely used stainless steels within the agri-food domain and to assess its anti-adhesive properties against various pathogens, especially on stainless steel 316L. Additionally, investigations into auto-aggregation and co-aggregation were also conducted. Plate count methodologies revealed increased biofilm formation by E. mundtii A2 on 316L, followed by 304L. Scanning electron microscopy (SEM) analysis revealed a dense yet thin biofilm layer, playing a critical role in reducing the adhesion of L. monocytogenes CECT 4032 and Staphylococcus aureus CECT 976, with a significant reduction of ≈ 2 Log CFU/cm2. However, Gram-negative strains, P. aeruginosa ATCC 27853 and E. coli ATCC 25922, exhibit modest adhesion reduction (~ 0.7 Log CFU/cm2). The findings demonstrate the potential of applying E. mundtii A2 biofilms as an effective strategy to reduce the adhesion and propagation of potentially pathogenic bacterial species on stainless steel 316L.

Size Effects of Copper Oxide Nanoparticles on Boosting Soybean Growth via Differentially Modulating Nitrogen Assimilation

Nanoscale agrochemicals have been widely used in sustainable agriculture and may potentially affect the nitrogen fixation process in legume crops. The present study investigated the size-effects of copper oxide nanoparticles (CuO NPs) on nitrogen assimilation in soybean (G. max (L.) Merrill) plants, which were treated with different sizes (20 and 50 nm) of CuO NPs at low use doses (1 and 10 mg/kg) for 21 days under greenhouse conditions. The results showed that 50 nm CuO NPs significantly increased the fresh biomass more than 20 nm CuO NPs achieved at 10 mg/kg. The activities of N assimilation-associated enzymes and the contents of nitrogenous compounds, including nitrates, proteins, and amino acids, in soybean tissues were greatly increased across all the CuO NP treatments. The use doses of two sizes of CuO NPs had no impact on the Cu contents in shoots and roots but indeed increased the Cu contents in soils in a dose-dependent fashion. Overall, our findings demonstrated that both 20 and 50 nm CuO NPs could positively alter soybean growth and boost N assimilation, furthering our understanding that the application of nanoscale micro-nutrient-related agrochemicals at an optimal size and dose will greatly contribute to increasing the yield and quality of crops.

Alleviated lead toxicity in rice plant by co-augmented action of genome doubling and TiO2 nanoparticles on gene expression, cytological and physiological changes

Lead is a very toxic and futile heavy metal for rice plants because of its injurious effects on plant growth and metabolic processes. Polyploidy or whole genome doubling increases the ability of plants to withstand biotic and abiotic stress. Considering the beneficial effects of nanoparticles and tetraploid rice, this research was conducted to examine the effectiveness of tetraploid and titanium dioxide nanoparticles (TiO2 NPs) in mitigating the toxic effects of lead. A diploid (E22-2x) and it's tetraploid (T-42) rice line were treated with Pb (200 μM) and TiO2 NPs (15 mg L-1). Lead toxicity dramatically reduced shoot length (16 % and 4 %) and root length (17 % and 9 %), biological yield (55 % and 36 %), and photosynthetic activity, as evidenced by lower levels of chlorophyll a and b (30 % and 9 %) in E-22 and T-42 rice cultivars compared to the control rice plants, respectively. Furthermore, lead toxicity amplified the levels of reactive oxygen species (ROS), such as malondialdehyde and H2O2, while decreasing activities of all antioxidant enzymes, such as superoxidase, peroxidase, and glutathione predominately in the diploid cultivar. Transmission electron microscopy and semi-thin section observations revealed that Pb-treated cells in E22-2x had more cell abnormalities than T-42, such as irregularly shaped mitochondria, cell wall, and reduced root cell size. Polyploidy and TiO2 reduced Pb uptake in rice cultivars and expression levels of metal transporter genes such as OsHMA9 and OsNRAMP5. According to the findings, genome doubling alleviates Pb toxicity by reducing Pb accumulation, ROS, and cell damage. Tetraploid rice can withstand the toxic effect of Pb better than diploid rice, and TiO2 NPs can alleviate the toxic impact of Pb. Our study findings act as a roadmap for future research endeavours, directing the focus toward risk management and assessing long-term impacts to balance environmental sustainability and agricultural growth.

Type VI secretion system drives bacterial diversity and functions in multispecies biofilms

Type VI secretion system (T6SS) plays an essential role in interspecies interactions and provides an advantage for a strain with T6SS in multispecies biofilms. However, how T6SS drives the bacterial community structure and functions in multispecies biofilms still needs to be determined. Using gene deletion and Illumina sequencing technique, we estimated bacterial community responses in multispecies biofilms to T6SS by introducing T6SS-containing Pseudomonas putida KT2440. Results showed that the niche structure shifts of multispecies biofilms were remarkably higher in the presence of T6SS than in the absence of T6SS. The presence of T6SS significantly drove the variation in microbial composition, reduced the alpha-diversity of bacterial communities in multispecies biofilms, and separately decreased and increased the relative abundance of Proteobacteria and Bacteroidota. Co-occurrence network analysis with inferred putative bacterial interactions indicated that P. putida KT2440 mainly displayed strong negative associations with the genera of Psychrobacter, Cellvibrio, Stenotrophomonas, and Brevundimonas. Moreover, the function redundancy index of the bacterial community was strikingly higher in the presence of T6SS than in the absence of T6SS, regardless of whether relative abundances of bacterial taxa were inhibited or promoted. Remarkably, the increased metabolic network similarity with T6SS-containing P. putida KT2440 could enhance the antibacterial activity of P. putida KT2440 on other bacterial taxa. Our findings extend knowledge of microbial adaptation strategies to potential bacterial weapons and could contribute to predicting biodiversity loss and change in ecological functions caused by T6SS.

Can nanotechnology improve the application of bioherbicides?

Bioherbicides are composed of microorganisms or natural compounds and are used for weed control; however, they have specific weaknesses and constraints that hinder their development and success under field conditions. Nanotechnology can help to overcome these limitations by providing a good starting point for the design of specific formulations and carriers that minimize the deficiencies of natural compounds and microorganisms, such as low solubility, short shelf life or a loss of viability. In addition, nanoformulations can help to improve the efficacy of bioherbicides by increasing their effectiveness and bioavailability, reducing the amount required for a treatment, and enhancing their ability to target specific weeds while preserving the crop. However, it is important to choose the right materials and nanodevices depending on specific needs and considering several factors inherent to nanomaterials such as production cost, safety or possible toxic effects. © 2023 Society of Chemical Industry.

Phosphate-solubilizing bacteria: Their agroecological function and optimistic application for enhancing agro-productivity

Phosphorus (P) is a limiting nutrient in the soil-plant nutrient cycling. Although the exogenous application of chemical P fertilizers can satisfy crop P requirements during critical growth phases. While excessive P fertilizers use results in low phosphorus acquisition efficiency (PAE), it has serious environmental consequences and hastens the depletion of P mineral reserves. Phosphate-solubilizing bacteria (PSB) have the potential to make insoluble phosphate available to plants through solubilization and mineralization, increasing crop yields while maintaining environmental sustainability. Existing reviews mainly focus on the beneficial effects of PSB on crop performance and related mechanisms, while few of them elucidate the action mechanisms of PSB in soil-microbe-plant interactions for crop cultivation with high yield efficiency. Hence, this study provides a comprehensive review of the physicochemical and molecular mechanisms (e.g., root exudates, extracellular polysaccharides, organic acids, phosphatases, and phosphate-specific transport systems) of PSB to facilitate the P cycle in the soil-plant systems. Further, the potential of commercial applications of PSB (e.g., genetic engineering, seed priming and coating) are also discussed in order to highlight their contribution to sustainable agriculture. Finally, existing challenges and future prospects in agricultural applications are proposed. In conclusion, we firmly believe that PSB represent a highly significant biotechnological tool for enhancing agricultural productivity and offers a wide range of extensive potential applications.

Visualization of root extracellular traps in an ectomycorrhizal woody plant (Pinus densiflora) and their interactions with root-associated bacteria

MAIN CONCLUSION

Extracellular traps in the primary root of Pinus densiflora contribute to root-associated bacterial colonization. Trapped rhizobacteria induce the production of reactive oxygen species in root-associated, cap-derived cells. Ectomycorrhizal (ECM) woody plants, such as members of Pinaceae and Fagaceae, can acquire resistance to biotic and abiotic stresses through the formation of mycorrhiza with ECM fungi. However, germinated tree seedlings do not have mycorrhizae and it takes several weeks for ectomycorrhizae to form on their root tips. Therefore, to confer protection during the early growth stage, bare primary roots require defense mechanisms other than mycorrhization. Here, we attempted to visualize root extracellular traps (RETs), an innate root defense mechanism, in the primary root of Pinus densiflora and investigate the interactions with root-associated bacteria isolated from ECM and fine non-mycorrhizal roots. Histological and histochemical imaging and colony-forming unit assays demonstrated that RETs in P. densiflora, mainly consisting of root-associated, cap-derived cells (AC-DCs) and large amounts of root mucilage, promote bacterial colonization in the rhizosphere, despite also having bactericidal activity via extracellular DNA. Four rhizobacterial strains retarded the mycelial growth of a pathogenic strain belonging to the Fusarium oxysporum species complex in dual culture assay. They also induced the production of reactive oxygen species (ROS) from host tree AC-DCs without being excluded from the rhizosphere of P. densiflora. Applying three Paraburkholderia strains, especially PM O-EM8 and PF T-NM22, showed significant differences in the ROS levels from the control group. These results reveal the indirect contributions of rhizobacteria to host root defense and suggest that root-associated bacteria could be a component of RETs as a first line of defense against root pathogens in the early growth stage of ECM woody plants.

Nano-Biofertilizer Formulations for Agriculture: A Systematic Review on Recent Advances and Prospective Applications

In the twenty-first century, nanotechnology has emerged as a potentially game-changing innovation. Essential minerals are mostly unavailable in modern cropping systems without the application of synthetic fertilizers, which have a serious negative impact on the ecosystem. This review focuses on the coupling of nanoparticles with biofertilizers to function as nano-biofertilizers (NBFs), which may ensure world food security in the face of the rising population. The inoculation of plants with NBFs improves plant development and resistance to stress. Metallic nanoparticles as well as organic components comprising polysaccharide and chitosan may be encapsulated, utilizing microbe-based green synthesis to make NBFs, which circumvents the limitations of conventional chemical fertilizers. The application of NBFs is just getting started, and shows more promise than other approaches for changing conventional farming into high-tech "smart" farming. This study used bibliographic analysis using Web of Science to find relevant papers on "nano biofertilizers", "plants", and "agriculture". These subjects have received a lot of attention in the literature, as shown by the co-citation patterns of these publications. The novel use of nanotechnology in agriculture is explored in this research work, which makes use of the unique characteristics of nanoscale materials to address urgent concerns including nutrient delivery, crop protection, and sustainable farming methods. This study attempts to fill in some of the gaps in our knowledge by discussing the formulation, fabrication, and characterization of NBFs, as well as elucidating the mechanisms by which NBFs interact with plants and how this benefits the ability of the plant to withstand biotic and abiotic stress brought about by climate change. This review also addresses recent developments and future directions in farming using NBF formulations in the field.

Microbial Biofilms: Applications, Clinical Consequences, and Alternative Therapies

Biofilms are complex communities of microorganisms that grow on surfaces and are embedded in a matrix of extracellular polymeric substances. These are prevalent in various natural and man-made environments, ranging from industrial settings to medical devices, where they can have both positive and negative impacts. This review explores the diverse applications of microbial biofilms, their clinical consequences, and alternative therapies targeting these resilient structures. We have discussed beneficial applications of microbial biofilms, including their role in wastewater treatment, bioremediation, food industries, agriculture, and biotechnology. Additionally, we have highlighted the mechanisms of biofilm formation and clinical consequences of biofilms in the context of human health. We have also focused on the association of biofilms with antibiotic resistance, chronic infections, and medical device-related infections. To overcome these challenges, alternative therapeutic strategies are explored. The review examines the potential of various antimicrobial agents, such as antimicrobial peptides, quorum-sensing inhibitors, phytoextracts, and nanoparticles, in targeting biofilms. Furthermore, we highlight the future directions for research in this area and the potential of phytotherapy for the prevention and treatment of biofilm-related infections in clinical settings.

Ameliorating Drought Effects in Wheat Using an Exclusive or Co-Applied Rhizobacteria and ZnO Nanoparticles

Drought is a major abiotic factor and affects cereal-based staple food production and reliability in developing countries such as Pakistan. To ensure a sustainable and consistent food supply, holistic production plans involving the integration of several drought mitigation approaches are required. Using a randomized complete block design strategy, we examined the drought-ameliorating characteristics of plant growth-promoting rhizobacteria (PGPR) and nanoparticles (NPs) exclusively or as a combined application (T4) through three stages (D1, D2, and D3) of wheat growth (T1, control). Our field research revealed that Azospirillum brasilense alone (T2) and zinc oxide NPs (T3) improved wheat plant water relations, chlorophyll, proline, phenolics and grain quality, yield, and their allied traits over the stressed treatments. Specifically, the best outcome was observed in the combined treatment of PGPR and ZnO NPs (T4). Interestingly, the combined treatment delivered effective drought mitigation through enhanced levels of antioxidants (15% APX, 27% POD, 35% CAT, 38% PPO and 44% SOD) over controls at the grain-filling stage (GFS, D3 × T1). The 40% improvements were recorded under the combined treatment at GFS over their respective controls. Their combined usage (PGPR and ZnO NPs) was concluded as an effective strategy for building wheat resilience under drought, especially in arid and semi-arid localities.

Genotype-Specific Recruitment of Rhizosphere Bacteria From Sandy Loam Soil for Growth Promotion of Cucumis sativus var. hardwickii

The composition and structure of the rhizosphere microbiome is affected by many factors, including soil type, genotype, and cultivation time of the plant. However, the interaction mechanisms among these factors are largely unclear. We use culture-independent 16S rRNA amplicon sequencing to investigate the rhizosphere bacterial composition and the structure of cultivated cucumber Xintaimici (XT) and wild-type cucumber Cucumis sativus var. hardwickii (HD) in four kinds of soils. We found that soil type, cultivation time, and genotype affected the composition and structure of cucumber rhizosphere bacterial communities. Notably, HD showed better physiological features in sandy soil and sandy loam soil than it did in black soil and farm soil at 50 days post-sowing, which was due to its stronger recruitment ability to Nitrospira, Nocardioides, Bacillus, and Gaiella in sandy soil, and more Tumebacillus, Nitrospira, and Paenibacillus in sandy loam soil. Meanwhile, we also found that HD showed a better recruiting capacity for these bacterial genera than XT in both sandy soil and sandy loam soil. Functional predictions indicated that these bacteria might have had stronger root colonization ability and then promoted the growth of cucumbers by enhancing nitrogen metabolism and active metabolite secretion. In this study, our findings provided a better insight into the relationship between cucumber phenotype, genotype, and the rhizosphere bacterial community, which will offer valuable theoretical references for rhizosphere microbiota studies and its future application in agriculture.

Bacterial extracellular matrix as a natural source of biotechnologically multivalent materials

The extracellular matrix (ECM) is an intricate megastructure made by bacterial cells to form architecturally complex biostructures called biofilms. Protection of cells, modulation of cell-to-cell signalling, cell differentiation and environmental sensing are functions of the ECM that reflect its diverse chemical composition. Proteins, polysaccharides and eDNA have specific functionalities while cooperatively interacting to sustain the architecture and biological relevance of the ECM. The accumulated evidence on the chemical heterogeneity and specific functionalities of ECM components has attracted attention because of their potential biotechnological applications, from agriculture to the water and food industries. This review compiles information on the most relevant bacterial ECM components, the biophysical and chemical features responsible for their biological roles, and their potential to be further translated into biotechnological applications.