Perspectives of Microbial Inoculation for Sustainable Development and Environmental Management

Starvation from within: How heavy metals compete with essential nutrients, disrupt metabolism, and impair plant growth

Nutrient starvation is a critical consequence of heavy metal toxicity, severely impacting plant health and productivity. This issue arises from various sources, including industrial activities, mining, agricultural practices, and natural processes, leading to the accumulation of metals such as aluminum (Al), arsenic (As), cadmium (Cd), chromium (Cr), lead (Pb), mercury (Hg), and nickel (Ni) in soil and water. Heavy metal exposure disrupts key physiological processes, particularly nutrient uptake and transport, resulting in nutrient imbalances within the plant. Essential nutrients are often unavailable or improperly absorbed due to metal chelation and interference with transporter functions, exacerbating nutrient deficiencies. This nutrient starvation, coupled with oxidative stress induced by heavy metals, manifests in impaired photosynthesis, stunted growth, and reduced crop yields. This review presents important insights into the molecular mechanisms driving nutrient deprivation in plants exposed to heavy metals, emphasizing the roles of transporters, transcription factors, and signaling pathways. It also examines the physiological and biochemical effects, such as chlorosis, necrosis, and altered metabolic activities. Lastly, we explore strategies to mitigate heavy metal-induced nutrient starvation, including phytoremediation, soil amendments, genetic approaches, and microbial interventions, offering insights for enhancing plant resilience in contaminated soils.

Novel insights into the effect of arbuscular mycorrhizal fungi inoculation in soils under long-term biosolids application: Emphasis on antibiotic and metal resistance genes, and mobile genetic elements

The application of biosolids can improve soil fertility and crop productivity but also accompanies risks of heavy metals and antibiotics introduction. In the presence of heavy metals contamination, using arbuscular mycorrhizal fungi (AMF) is a promising strategy to enhance soil microbial community stability and plant tolerance resistance to heavy metals, and to reduce the spread of antibiotic resistance genes (ARGs). The present study investigated the impacts of AMF inoculation on soil and plant heavy metal contents, and soil microbial communities by pot experiments. The results showed that AMF inoculation significantly enhanced plant biomass, and reduced soil and plant heavy metals contents. While AMF inoculation did not alter bacterial and fungal community compositions, it increased bacterial diversity at higher biosolids concentrations. Notably, AMF inoculation enhanced microbial network complexity and increased keystone taxa abundance. Furthermore, several beneficial microorganisms with high resistance to heavy metals were enriched in AMF-inoculated soils. Metagenomic analysis revealed a reduction in the mobile genetic element (MGE) gene IS91 in AMF-inoculated soils and an increase in heavy metal resistance genes compared to soils without AMF. The possibility of reduction in MGE-mediated spread of ARGs is one of the key findings of this study. As a caution, this study also detected enrichment of few ARGs in high biosolids-amended soils with AMF inoculation. Overall, AMF inoculation could be a valuable strategy in agriculture for mitigating the environmental risks associated with biosolids, heavy metals and antibiotic resistance, thereby promoting sustainable soil management and health.

Hypersaline organic wastewater treatment: Biotechnological advances and engineering challenges

The sustainable treatment of hypersaline organic wastewater (HSOW) remains a significant challenge in industrial wastewater management, as conventional approaches often fail to meet stringent discharge standards and low-carbon sustainability targets. Halotolerant and halophilic microbial strains offer promising solutions, yet their application is hindered by limited stress resistance, thus hindering effective treatment and achieving near-zero liquid discharge. In this review, we systematically examine endogenous strategies, such as microbial mutualism and genetic engineering, alongside exogenous approaches, including functional materials, electrical and magnetic stimulation, and 3D bioprinting, to improve microbial resilience in hypersaline environments. Furthermore, we propose an integrated treatment framework that combines physicochemical and biochemical processes, leveraging biological detoxification and biological desalination to enhance the treatment of HSOW while minimizing environmental impact and carbon emissions. By advancing the understanding of microbial stress adaptation and optimization strategies, this review provides critical insights into the development of sustainable, low-carbon wastewater treatment solutions.

Synthetic Microbial Communities Enhance Pepper Growth and Root Morphology by Regulating Rhizosphere Microbial Communities

Synthetic microbial community (SynCom) application is efficient in promoting crop yield and soil health. However, few studies have been conducted to enhance pepper growth via modulating rhizosphere microbial communities by SynCom application. This study aimed to investigate how SynCom inoculation at the seedling stage impacts pepper growth by modulating the rhizosphere microbiome using high-throughput sequencing technology. SynCom inoculation significantly increased shoot height, stem diameter, fresh weight, dry weight, chlorophyll content, leaf number, root vigor, root tips, total root length, and root-specific surface area of pepper by 20.9%, 36.33%, 68.84%, 64.34%, 29.65%, 27.78%, 117.42%, 35.4%, 21.52%, and 39.76%, respectively, relative to the control. The Chao index of the rhizosphere microbial community and Bray-Curtis dissimilarity of the fungal community significantly increased, while Bray-Curtis dissimilarity of the bacterial community significantly decreased by SynCom inoculation. The abundances of key taxa such as Scedosporium, Sordariomycetes, Pseudarthrobacter, norankSBR1031, and norankA4b significantly increased with SynCom inoculation, and positively correlated with indices of pepper growth. Our findings suggest that SynCom inoculation can effectively enhance pepper growth and regulate root morphology by regulating rhizosphere microbial communities and increasing key taxa abundance like Sordariomycetes and Pseudarthrobacter, thereby benefiting nutrient acquisition, resistance improvement, and pathogen resistance of crops to ensure sustainability.

Harnessing bacterial endophytes for environmental resilience and agricultural sustainability

In the current era of environmental disasters and the necessity of sustainable development, bacterial endophytes have gotten attention for their role in improving agricultural productivity and ecological sustainability. This review explores the multifaceted contributions of bacterial endophytes to plant health and ecosystem sustainability. Bacterial endophytes are invaluable sources of bioactive compounds, promising breakthroughs in medicine and biotechnology. They also serve as natural biocontrol agents, reducing the need for synthetic fertilizers and fostering environmentally friendly agricultural practices. It provides eco-friendly solutions that align with the necessity of sustainability since they can improve pest management, increase crop resilience, and facilitate agricultural production. This review also underscores bacterial endophytes' contribution to promoting sustainable and green industrial productions. It also presented how incorporating these microorganisms into diverse industrial sectors can harmonize humankind with ecological stability. The potential of bacterial endophytes has been largely untapped, presenting an opportunity for pioneering advancements in sustainable industrial applications. Their importance caught attention as they provided innovative solutions to the challenging problems of the new era. This review sheds light on the remarkable potential of bacterial endophytes in various industrial sectors. Further research is imperative to discover their multifaceted potential. It will be essential to delve deeper into their mechanisms, broaden their uses, and examine their long-term impacts.

Microbial Consortia: Promising Tool as Plant Bioinoculants for Agricultural Sustainability

In the present scenario, growing population demands more food, resulting in the need for sustainable agriculture. Numerous approaches are explored in response to dangers and obstacles to sustainable agriculture. A viable approach is to be exploiting microbial consortium, which generate diverse biostimulants with growth-promoting characteristics for plants. These bioinoculants play an indispensable role in optimizing nutrient uptake efficiency mitigating environmental stress. Plant productivity is mostly determined by the microbial associations that exist at the rhizospheric region of plants. The engineered consortium with multifunctional attributes can be effectively employed to improve crop growth efficacy. A number of approaches have been employed to identify the efficient consortia for plant growth and enhanced crop productivity. Various plant growth-promoting (PGP) microbes with host growth-supporting characteristics were investigated to see if they might work cohesively and provide a cumulative effect for improved growth and crop yield. The effective microbial consortia should be assessed using compatibility tests, pot experimentation techniques, generation time, a novel and quick plant bioassay, and sensitivity to external stimuli (temperature, pH). The mixture of two or more microbial strains found in the root microbiome stimulates plant growth and development. The present review deals with mechanism, formulation, inoculation process, commercialization, and applications of microbial consortia as plant bioinoculants for agricultural sustainability.

Do chromium-resistant bacterial symbionts of hyperaccumulator Callitriche cophocarpa support their host in phytobial remediation of water?

Callitriche cophocarpa Sendtn. is a macrophyte widely distributed in aquatic systems of the temperate climate zone and a known hyperaccumulator of chromium. Ten pure symbiotic bacterial isolates of C. cophocarpa were obtained and identified. Three of the isolates showed the highest resistance to Cr(VI): Microbacterium sp. (Ct1), Aeromonas sp. (Ct3) and Acinetobacter sp. (Ct6). Acinetobacter sp. (Ct6) was able to survive up to a concentration of 104 mg/L (2 mM). The isolates were also able to effectively detoxify Cr(VI) by reducing it to Cr(III). We tested whether inoculation of plants with a consortium consisting of Ct1, Ct3 and Ct6 affects: (1) the phytoextraction of chromium from leachates, (2) the physiological state of plants after Cr(VI) treatment. The solutions were landfill leachates and contained 10.7 mg/L of Cr(VI) - an amount 530 times exceeding the legal limits. We influenced the plants with Cr in two steps, each lasting for 10 days, first using mature shoots and then apical ones. The highest Cr content concomitant with the highest bioconcentration factor (BCF) were found in the inoculated plants: 1274 and 119 mg/kg dry mass (d.m.), respectively. The physiological status of the plants was assessed by biometric tests and advanced chlorophyll fluorescence analyses. The photosynthetic activity of mature shoots was influenced by Cr(VI) more negatively than that of young apical shoots. The inoculation with the bacterial consortium significantly reduced the negative effect of Cr(VI) on mature organs. In some cases the inoculated mature plants exhibited photosynthetic activity that was even higher than in the control plants. The results unequivocally show a beneficial effect of C. cophocarpa inoculation with the tested isolates resulting in a significant improvement of the phytoremediation properties of this aquatic chromium hyperaccumulator.

Lose-lose consequences of bacterial community-driven invasions in soil

BACKGROUND

Community-driven invasion, also known as community coalescence, occurs widely in natural ecosystems. Despite that, our knowledge about the process and mechanisms controlling community-driven invasion in soil ecosystems is lacking. Here, we performed a set of coalescence experiments in soil microcosms and assessed impacts up to 60 days after coalescence by quantifying multiple traits (compositional, functional, and metabolic) of the invasive and coalescent communities.

RESULTS

Our results showed that coalescences significantly triggered changes in the resident community's succession trajectory and functionality (carbohydrate metabolism), even when the size of the invasive community is small (~ 5% of the resident density) and 99% of the invaders failed to survive. The invasion impact was mainly due to the high suppression of constant residents (65% on average), leading to a lose-lose situation where both invaders and residents suffered with coalescence. Our results showed that surviving residents could benefit from the coalescence, which supports the theory of "competition-driven niche segregation" at the microbial community level. Furthermore, the result showed that both short- and long-term coalescence effects were predicted by similarity and unevenness indexes of compositional, functional, and metabolic traits of invasive communities. This indicates the power of multi-level traits in monitoring microbial community succession. In contrast, the varied importance of different levels of traits suggests that competitive processes depend on the composition of the invasive community.

CONCLUSIONS

Our results shed light on the process and consequence of community coalescences and highlight that resource competition between invaders and residents plays a critical role in soil microbial community coalescences. These findings provide valuable insights for understanding and predicting soil microbial community succession in frequently disturbed natural and agroecosystems. Video Abstract.

Environmental microbiome engineering for the mitigation of climate change

Environmental microbiome engineering is emerging as a potential avenue for climate change mitigation. In this process, microbial inocula are introduced to natural microbial communities to tune activities that regulate the long-term stabilization of carbon in ecosystems. In this review, we outline the process of environmental engineering and synthesize key considerations about ecosystem functions to target, means of sourcing microorganisms, strategies for designing microbial inocula, methods to deliver inocula, and the factors that enable inocula to establish within a resident community and modify an ecosystem function target. Recent work, enabled by high-throughput technologies and modeling approaches, indicate that microbial inocula designed from the top-down, particularly through directed evolution, may generally have a higher chance of establishing within existing microbial communities than other historical approaches to microbiome engineering. We address outstanding questions about the determinants of inocula establishment and provide suggestions for further research about the possibilities and challenges of environmental microbiome engineering as a tool to combat climate change.

Can arbuscular mycorrhizal fungi and rhizobacteria facilitate 33P uptake in maize plants under water stress?

Arbuscular mycorrhizal fungi (AMF) and plant growth-promoting rhizobacteria (PGPR) are able to provide key ecosystem services, protecting plants against biotic and abiotic stresses. Here, we hypothesized that a combination of AMF (Rhizophagus clarus) and PGPR (Bacillus sp.) could enhance ³³P uptake in maize plants under soil water stress. A microcosm experiment using mesh exclusion and a radiolabeled phosphorus tracer (³³P) was installed using three types of inoculation: i) only AMF, ii) only PGPR, and iii) a consortium of AMF and PGPR, alongside a control treatment without inoculation. For all treatments, a gradient of three water-holding capacities (WHC) was considered i) 30% (severe drought), ii) 50% (moderate drought), and iii) 80% (optimal condition, no water stress). In severe drought conditions, AMF root colonization of dual-inoculated plants was significantly lower compared to individual inoculation of the AMF, whilst ³³P uptake by dual-inoculated plants or plants inoculated with bacteria was 2.4-fold greater than the uninoculated treatment. Under moderate drought conditions the use of AMF promoted the highest ³³P uptake by plants, increasing it by 2.1-fold, when compared to the uninoculated treatment. Without drought stress, AMF showed the lowest ³³P uptake and, overall, plant P acquisition was lower for all inoculation types when compared to the severe and moderate drought treatments. The total shoot P content was modulated by the water-holding capacity and inoculation type, with the lowest values observed under severe drought and the highest values under moderate drought. The highest soil electrical conductivity (EC) values were found under severe drought in AMF-inoculated plants and the lowest EC for no drought in single or dual-inoculated plants. Furthermore, water-holding capacity influenced the total soil bacterial and mycorrhizal abundance over time, with the highest abundances being found under severe and moderate drought. This study demonstrates that the positive influence of microbial inoculation on ³³P uptake by plants varied with soil water gradient. Furthermore, under severe stress conditions, AMF invested more in the production of hyphae, vesicles and spore production, indicating a significant carbon drain from the host plant as evidenced by the lack of translation of increased ³³P uptake into biomass. Therefore, under severe drought the use of bacteria or dual-inoculation seems to be more effective than individual AMF inoculation in terms of ³³P uptake by plants, while under moderate drought, the use of AMF stood out.

Bacteria isolated from e-waste soil enhance plant growth and mobilize trace metals in e-waste-amended soils

Worldwide accumulation of e-waste poses a major threat to environmental health. However, printed circuit boards contain precious metals, such as gold, and silver, and also contain micronutrient metal elements, such as Fe, Cu, Zn, etc. Therefore, the present study investigated the effects of e-waste-tolerant bacteria (ETB) on promoting plant growth in e-waste-amended soils and mobilizing trace metals into the plants. For this, a total of 18 bacteria were isolated and screened for e-waste tolerance. Screening for plant growth-promoting properties revealed the production of indole-3-acetic acid-like compounds, siderophore production, and phosphate solubilization. Identification based on 16S rRNA gene sequencing revealed that all isolates belonged to the genus Bacillus. Pot experiment revealed that the treated seeds showed the enhancement of chili plants root growth ranging from 106.55 to 208.07% compared to control plants (e-waste) and 0.0 to 47.90% (without e-waste). A similar enhancement was also observed in the shoot length, and size of the leaf compared to e-waste amended control plants. Inoculation of ETB significantly (p < 0.05) mobilized Fe, Zn, Cu, and Ni into chili plants. The identified ETB could be used to mitigate the toxicity posed by the e-waste, enhancing plant growth and mobilization of micronutrients into plants from e-waste.

Assessment of beneficial fungal microorganism's bio-efficacy in stimulating morphological and physiological parameters of Allium cepa plants grown in soil amended with fish wastes

BACKGROUND

The increase in the human consumption of fish results in the production of organic fish wastes (FW). For enhanced soil fertility and plant growth at a lower cost and without the negative impacts of chemical fertilizers, these wastes could be employed as a valuable organic fertilizer. To determine the synergistic bio-efficacy of Trichoderma sp. and arbuscular mycorrhizal (AM) fungi in stimulating the morphological and physiological characteristics of FW-fertilized Alium cepa, as well as to investigate their involvement in boosting soil fertility, the current study was carried out. Overall, eight treatments were applied as follows: AM, Trichoderma sp., AM + Trichoderma sp., FW, AM + FW, Trichoderma sp. + FW, AM + Trichoderma sp. + FW, and control. Growth and physiological assessments of onion plants were taken after 8 weeks from FW application.

RESULTS

Our results showed that FW application combined with AM fungi and Trichoderma sp. inoculations increased aggregate stability of the soil (glomalin content) and soil chitinase activity. Moreover, using the bio-inoculations along with FW amendments significantly (p < 0.05) improved the photosynthetic pigments, protein, carbohydrates, and nutrients content of onion plants. It's interesting to note that the triple interaction of AM + Trichoderma sp. + FW led to the greatest increase in plant height, root length, number of leaves, and leaf area as well as total fresh and dry weights of shoots and roots. Besides, AM fungal colonization was at its highest percentage with Trichoderma sp. inoculation, although this percentage decreased with FW addition.

CONCLUSION

We concluded that the combined treatments of AM fungi and Trichoderma sp. along with FW application to the soil can be proposed as a successful strategy for plant performance in nutrient-deficient soils as both fungal inoculants are capable of degrading these wastes and converting them into manure suitable for farming so plants can uptake the minerals effortlessly.

Cell-free microbial culture filtrates as candidate biostimulants to enhance plant growth and yield and activate soil- and plant-associated beneficial microbiota

In this work we compiled information on current and emerging microbial-based fertilization practices, especially the use of cell-free microbial culture filtrates (CFs), to promote plant growth, yield and stress tolerance, and their effects on plant-associated beneficial microbiota. In addition, we identified limitations to bring microbial CFs to the market as biostimulants. In nature, plants act as metaorganisms, hosting microorganisms that communicate with the plants by exchanging semiochemicals through the phytosphere. Such symbiotic interactions are of high importance not only for plant yield and quality, but also for functioning of the soil microbiota. One environmentally sustainable practice to increasing crop productivity and/or protecting plants from (a)biotic stresses while reducing the excessive and inappropriate application of agrochemicals is based on the use of inoculants of beneficial microorganisms. However, this technology has a number of limitations, including inconsistencies in the field, specific growth requirements and host compatibility. Beneficial microorganisms release diffusible substances that promote plant growth and enhance yield and stress tolerance. Recently, evidence has been provided that this capacity also extends to phytopathogens. Consistently, soil application of microbial cell-free culture filtrates (CFs) has been found to promote growth and enhance the yield of horticultural crops. Recent studies have shown that the response of plants to soil application of microbial CFs is associated with strong proliferation of the resident beneficial soil microbiota. Therefore, the use of microbial CFs to enhance both crop yield and stress tolerance, and to activate beneficial soil microbiota could be a safe, efficient and environmentally friendly approach to minimize shortfalls related to the technology of microbial inoculation. In this review, we compile information on microbial CFs and the main constituents (especially volatile compounds) that promote plant growth, yield and stress tolerance, and their effects on plant-associated beneficial microbiota. In addition, we identify challenges and limitations for their use as biostimulants to bring them to the market and we propose remedial actions and give suggestions for future work.

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.

A biochemical, physiological and molecular evaluation of how the herbicide 2, 4-dichlorophenoxyacetic acid intercedes photosynthesis and diazotrophy in the cyanobacterium Nostoc muscorum Meg 1

Among the non-target microorganisms residing in crop fields that are potentially vulnerable to herbicides are cyanobacteria. They contribute to the maintenance of soil quality and fertility and hence are considered to be an important component of soil microflora. Consequently, the present study was aimed to check the influence of the herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) on some major parameters of carbon (CO₂) and nitrogen (N₂) fixations of a cyanobacterium Nostoc muscorum Meg 1 isolated from a rice field in Cherrapunji, Meghalaya, India. These include various photosynthetic pigments, the oxygen-evolving complex activity of the PSII, the protein contents of RuBisCO, D1 protein, isocitrate dehydrogenase (IDH), nitrogenase and glutamine synthetase (GS) enzymes, the heterocyst percentage, nitrogenase and GS enzyme activities, and production of total proteins and carbohydrates in the cyanobacterium in a varying range of 50 to 125 ppm doses of 2,4-D. The mRNA levels of several proteins were also analyzed. Besides carotenoid concentration that enhanced at 50 ppm, all other parameters were compromised by 2,4-D in a dose-dependent manner resulting in a reduction in photosynthetic and N₂-fixing activities. The negative effect on N₂-fixation was partly due to compromised IDH activity. RT-PCR analysis further showed that these negative effects were initiated at transcription levels as mRNA contents of all enzymes studied were found compromised under 2,4-D exposure. The scanning and transmission electron microscopy further revealed herbicide induced adverse changes in the morphology and ultrastructure of the organism. The significance of the work lies in its detailed analysis of the effect of 2,4-D at biochemical, physiological, and molecular levels.

The legacy of microbial inoculants in agroecosystems and potential for tackling climate change challenges

Microbial inoculations contribute to reducing agricultural systems' environmental footprint by supporting sustainable production and regulating climate change. However, the indirect and cascading effects of microbial inoculants through the reshaping of soil microbiome are largely overlooked. By discussing the underlying mechanisms of plant- and soil-based microbial inoculants, we suggest that a key challenge in microbial inoculation is to understand their legacy on indigenous microbial communities and the corresponding impacts on agroecosystem functions and services relevant to climate change. We explain how these legacy effects on the soil microbiome can be understood by building on the mechanisms driving microbial invasions and placing inoculation into the context of ecological succession and community assembly. Overall, we advocate that generalizing field trials to systematically test inoculants' effectiveness and developing knowledge anchored in the scientific field of biological/microbial invasion are two essential requirements for applying microbial inoculants in agricultural ecosystems to tackle climate change challenges.

Changes in the phyllosphere and rhizosphere microbial communities of soybean in the presence of pathogens

Soybean (Glycine max L.) is host to an array of foliar- and root-infecting pathogens that can cause significant yield losses. To provide insights into the roles of microorganisms in disease development, we evaluated the bacterial and fungal communities associated with the soybean rhizosphere and phyllosphere. For this, leaf and soil samples of healthy, Phytophthora sojae-infected and Septoria glycines-infected plants were sampled at three stages during the production cycle, and then subjected to 16S and Internal Transcribed Spacer (ITS) amplicon sequencing. The results indicated that biotic stresses did not have a significant impact on species richness and evenness regardless of growth stage. However, the structure and composition of soybean microbial communities were dramatically altered by biotic stresses, particularly for the fungal phyllosphere. Additionally, we cataloged a variety of microbial genera that were altered by biotic stresses and their associations with other genera, which could serve as biological indicators for disease development. In terms of soybean development, the rhizosphere and phyllosphere had distinct microbial communities, with the fungal phyllosphere most influenced by growth stage. Overall, this study characterized the phyllosphere and rhizosphere microbial communities of soybean, and described the impact of pathogen infection and plant development in shaping these bacterial and fungal communities.

Endophytic fungi: a tool for plant growth promotion and sustainable agriculture

Endophytic fungi are found in most, if not all, plant species on the planet. They colonise inner plant tissues without causing symptoms of disease, thus providing benefits to the host plant while also benefiting from this interaction. The global concern for the development of more sustainable agriculture has increased in recent years, and research has been performed to decipher ecology and explore the potential of endophytic interactions in plant growth. To date, many studies point to the positive aspects of endophytic colonisation, and in this review, such research is summarised based on the direct (acquisition of nutrients and phytohormone production) and indirect (induced resistance, production of antibiotics and secondary metabolites, production of siderophores and protection for abiotic and biotic stresses) benefits of endophytic colonisation. An in-depth discussion of the mechanisms is also presented.

Endophytic fungi: a tool for plant growth promotion and sustainable agriculture

Endophytic fungi are found in most, if not all, plant species on the planet. They colonise inner plant tissues without causing symptoms of disease, thus providing benefits to the host plant while also benefiting from this interaction. The global concern for the development of more sustainable agriculture has increased in recent years, and research has been performed to decipher ecology and explore the potential of endophytic interactions in plant growth. To date, many studies point to the positive aspects of endophytic colonisation, and in this review, such research is summarised based on the direct (acquisition of nutrients and phytohormone production) and indirect (induced resistance, production of antibiotics and secondary metabolites, production of siderophores and protection for abiotic and biotic stresses) benefits of endophytic colonisation. An in-depth discussion of the mechanisms is also presented.

Bioprospecting microwave-alkaline hydrolysate cocktail of defatted soybean meal and jackfruit peel biomass as carrier additive of molasses-alginate-bead biofertilizer

The extraction of soluble hydrolysate protein and sugar from a biomass cocktail of defatted soybean meal (DSM) and jackfruit peel (JP) was examined using microwave-alkaline hydrolysis by varying the NaOH concentrations (0.04–0.11 M) and residence times (2–11 min). Based on the central composite design, the optimized parameters were achieved at 0.084 M NaOH concentration (100 mL), for 8.7 min at 300 W microwave power level to obtain the highest protein (5.31 mg/mL) and sugar concentrations (8.07 mg/mL) with > 75% recovery. Both raw and detoxified hydrolysate (using activated carbon) were correspondingly biocompatible with Enterobacter hormaechei strain 40a (P > 0.05) resulting in maximal cell counts of > 10 log CFU/mL. The optimized hydrolysate was prepared as an additive in molasses-alginate bead encapsulation of strain 40a. Further evaluation on phosphate and potassium solubilization performance of the encapsulated strain 40a exhibited comparable results with those of free cell counterpart (P > 0.05). The DSM-JP hydrolysate cocktail holds potential as a carrier additive of encapsulated-cell bead biofertilizers in order to sustain bacterial cell quality and consequently improve crop growth and productivity.

Food systems at a watershed: Unlocking the benefits of technology and ecosystem symbioses

The current food systems require change to improve sustainability resilience. Humans need food and food requires natural resources which have been consistently reduced, destroyed, or eliminated during human development, and excessive during the last 50-70 years. Though essential, there has been less of a focus on the inter-relations and inter-dependences of our food supply with and on the world's eco-system and organisms. Integrating evidence for the importance of plants, the microbiota in plants, animals and humans and their reciprocal effects of their interactions on food systems is essential for creating more inclusive strategies for future food systems. This review examines the role of plants, microorganisms, plant-microbial, animal-microbial, and human-microbial interactions, their co-evolution on the food supply and human and eco-systems well-being. It also recognizes the contribution of indigenous knowledge for lasting protection of the land, managing resources and biodiversity and the usefulness of food processing for producing safe, tasty, and nutritious food sustainably. We demonstrate that new targets and priorities for harnessing science and technology for improving food and nutritional security and avoiding environmental degradation and biodiversity loss are urgently needed. For improved long-term sustainability, the benefits of technology and ecosystem interactions must be unlocked.

Bioactive Nutrient Fortified Fertilizer: A Novel Hybrid Approach for the Enrichment of Wheat Grains With Zinc

Zinc (Zn) is a critical micronutrient that synergizes nutrient use efficiency, and improves plant growth and human health. Low Zn bioavailability in soils affects produce quality and agricultural productivity worldwide ultimately inducing deficiency in humans and animals. Zn deficiency is a leading cause of malnutrition in underdeveloped countries where a widespread population depends upon staple cereals for daily intake of calories. Modern cereal cultivars are inherently low in Zn, eventually, plants need to be enriched with soil application of ZnSO₄, but due to higher fixation losses, it becomes an inefficient source. Rhizosphere microbiome contains Zn-solubilizing bacteria (ZSB) that improve Zn bioavailability, thus increase the root function, Zn uptake, and plant growth. Niha Corp developed a hybrid process of bioactive nutrient fortified fertilizer (BNFF), which has been used to formulate Zabardast Urea (ZU) by coating bioactive Zn (BAZ) and ZSB on urea. Data obtained for 15 wheat varieties from 119 farmer field demonstration plots and eight replicated trials on 42 locations across multi-environment conditions conclude that ZU significantly improved the plant biomass and yield by 12% over non-Zn control and produced grains with 57 μg/g Zn contents, which can meet a major part of the recommended dietary allowance (RDA) of humans. The study recommends that this microbe-mediated hybrid invention (ZU) is a feasible approach to boost Zn bioavailability and Zn use efficiency, with enhanced yield and quality that may contribute to improve human health. To the best of our knowledge, this is the first wide-scale field testing of Zn enrichment in the grains of bread wheat using an innovative BNFF Urea Z technology.

Consumer willingness to pay for plant-based foods produced using microbial applications to replace synthetic chemical inputs

Analysis of consumer preferences and willingness-to-pay (WTP) for sustainable foods produced using new agri-food technologies is required to enhance the uptake of innovations that accelerate the transition towards sustainable food systems. Consumers' willingness to buy new food products, with no or limited consumption experience, mainly depends on their food choice motivational orientations (promotion- vs prevention-orientation). The objective of this study was to elicit consumers' WTP for foods that are produced with microbial applications during the plant production phase with the aim to reduce the use of synthetic chemicals in crop farming, as well as to understand the associations of food choice motives, personal and socio-demographic factors with the WTP. We used contingent valuation to elicit consumers' WTP for three food products (wheat bread, consumer potatoes and tomato sauce) through online surveys. Data were collected from 291 consumers, primarily from Italy, Germany and the Netherlands. Descriptive statistics, latent variable modelling and logistic regression were used to analysis data. Results show that more than two-third of the respondents are willing to pay premiums of at least 0.11 euro per kg of food products for reductions in synthetic chemical use by at least 50% due to microbial applications. The amount of WTP increases with the level of reductions in synthetic chemical use. The majority of the respondents are promotion-oriented consumers in relation to their food involvement, and are more likely to pay premiums for the sustainably produced food products. Environmentally concerned consumers are also more likely to pay premiums, whereas health concerned consumers are not. This study contributes to understanding of consumers' attitude and perceived health risks towards foods obtained using microbial applications, and the heterogeneity of their preferences. Results provide insights for identifying potential buyers of foods produced using microbial applications, and to set prices according to the levels of consumers' WTP.

Enhanced Yield of Pepper Plants Promoted by Soil Application of Volatiles From Cell-Free Fungal Culture Filtrates Is Associated With Activation of the Beneficial Soil Microbiota

Plants communicate with microorganisms by exchanging chemical signals throughout the phytosphere. Such interactions are important not only for plant productivity and fitness, but also for terrestrial ecosystem functioning. It is known that beneficial microorganisms emit diffusible substances including volatile organic compounds (VOCs) that promote growth. Consistently, soil application of cell-free culture filtrates (CF) of beneficial soil and plant-associated microorganisms enhances plant growth and yield. However, how this treatment acts in plants and whether it alters the resident soil microbiota, are largely unknown. In this work we characterized the responses of pepper (Capsicum annuum L.) plants cultured under both greenhouse and open field conditions and of soil microbiota to soil application of CFs of beneficial and phytopathogenic fungi. To evaluate the contribution of VOCs occurring in the CFs to these responses, we characterized the responses of plants and of soil microbiota to application of distillates (DE) of the fungal CFs. CFs and their respective DEs contained the same potentially biogenic VOCs, and application of these extracts enhanced root growth and fruit yield, and altered the nutritional characteristics of fruits. High-throughput amplicon sequencing of bacterial 16S and fungal ITS rRNA genes of the soil microbiota revealed that the CF and DE treatments altered the microbial community compositions, and led to strong enrichment of the populations of the same beneficial bacterial and fungal taxa. Our findings show that CFs of both beneficial and phytopathogenic fungi can be used as biostimulants, and provide evidence that VOCs occurring in the fungal CFs act as mediators of the plants' responses to soil application of fungal CFs through stimulation of the beneficial soil microbiota.

Profiling of Plant Growth-Promoting Metabolites by Phosphate-Solubilizing Bacteria in Maize Rhizosphere

Microbial treatment has recently been attracting attention as a sustainable agricultural strategy addressing the current problems caused by unreasonable agricultural practices. However, the mechanism through which microbial inoculants promote plant growth is not well understood. In this study, two phosphate-solubilizing bacteria (PSB) were screened, and their growth-promoting abilities were explored. At day 7 (D7), the lengths of the root and sprout with three microbial treatments, M16, M44, and the combination of M16 and M44 (Com), were significantly greater than those with the non-microbial control, with mean values of 9.08 and 4.73, 7.15 and 4.83, and 13.98 and 5.68 cm, respectively. At day 14 (D14), M16, M44, and Com significantly increased not only the length of the root and sprout but also the underground and aboveground biomass. Differential metabolites were identified, and various amino acids, amino acid derivatives, and other plant growth-regulating molecules were significantly enhanced by the three microbial treatments. The profiling of key metabolites associated with plant growth in different microbial treatments showed consistent results with their performances in the germination experiment, which revealed the metabolic mechanism of plant growth-promoting processes mediated by screened PSB. This study provides a theoretical basis for the application of PSB in sustainable agriculture.

The individual and interactive role of arbuscular mycorrhizal fungi and Trichoderma viride on growth, protein content, amino acids fractionation, and phosphatases enzyme activities of onion plants amended with fish waste

The Green Revolution faced a great cost to meet ever-increasing demands for food, where indiscriminate use of agrochemicals resulted in non-friendly habitats. Therefore, the development of a sustainable approach to better crop production of onion seeds (Allium cepa L.) is very crucial. It is time to use organic waste as a replacement for agrochemicals by using arbuscular mycorrhizal fungi (AMF) and Trichoderma. Fish waste as representative of food waste acts as a leading cause of contamination of the environment. The interaction of AMF and Trichoderma viride on biomass, total soluble protein, mycorrhizal colonization, amino acids, phosphatases and phosphorus and nitrogen contents of onion plants grown in fish waste amended soil was studied. Fish waste has caused a slight increase in onions biomass, total free amino acids, and soluble protein content while with AMF and T. viride dual inoculation more increments were recorded; such increases were related to an increase in mycorrhizal colonization. T. viride application significantly increased the mycorrhizal colonization levels, but these were significantly reduced with waste addition. Analysis of amino acids in plants showed that their concentrations had changed as a result of waste addition combined with AMF and/or T. viride. The effectiveness of fish waste combined with low cost and health/environmental safety leads to a prediction that the introduction of fish waste coupled with fungi will become a more popular feature of agriculture in the future.

Marine associated microbial consortium applied to RBBR textile dye detoxification and decolorization: Combined approach and metatranscriptomic analysis

The combination of different microorganisms and their metabolisms makes the use of microbial consortia in bioremediation processes a useful approach. In this sense, this study aimed at structuring and selecting a marine microbial consortium for Remazol Brilliant Blue R (RBBR) detoxification and decolorization. Experimental design was applied to improve the culture conditions, and metatranscriptomic analysis to understand the enzymatic pathways. A promising consortium composed of Mucor racemosus CBMAI 847, Marasmiellus sp. CBMAI 1062, Bacillus subtilis CBMAI 707, and Dietzia maris CBMAI 705 was selected. This consortium showed 52% of detoxification and 86% of decolorization in the validation assays after seven days of incubation in the presence of 500 ppm of RBBR. Reduction in RBBR color and toxicity were achieved by biosorption and microbial metabolisms. Metatranscriptomic data indicate that the consortium was able to decolorize and breakdown the RBBR molecule using a coordinated action of oxidases, oxygenases, and hydrolases. Epoxide hydrolases and glyoxalases expression could be associated with the decrease in toxicity. The efficiency of this marine microbial consortium suggests their use in bioremediation processes of textile effluents.

Plant growth-promoting microbes — an industry view

Plant growth-promoting microbes can affect the plant microbiome, improving different properties of the plant such as yield and health. Many companies are commercializing these microbes as products called biologicals. Defining the product concept is one of the first and most important steps in making a biological product. Companies can use phenotyping and genotyping approaches to identify the microbe to make into a live bacterial product. Screening usually begins in the laboratory and often moves from high-throughput methods to more time and resource-intensive methods culminating in large scale field testing. Once the microbe is chosen, the fermentation process grows the bacteria to the necessary amounts, while the formulation process ensures a stable product in the desired form such as a liquid or powder. The products must show yield increases in the field over several seasons and conditions, but also must be easy to use and cost-effective to be adopted by farmers and other customers. Tying all these data together from the selection process to test results gives a customer a ‘reason to believe’ for the marketing and launch of a successful product.

Biocontrol of Two Bacterial Inoculant Strains and Their Effects on the Rhizosphere Microbial Community of Field-Grown Wheat

Biocontrol by inoculation with beneficial microbes is a proven strategy for reducing the negative effect of soil-borne pathogens. We evaluated the effects of microbial inoculants BIO-1 and BIO-2 in reducing soil-borne wheat diseases and in influencing wheat rhizosphere microbial community composition in a plot test. The experimental design consisted of three treatments: (1) Fusarium graminearum F0609 (CK), (2) F. graminearum + BIO-1 (T1), and (3) F. graminearum F0609 + BIO-2 (T2). The results of the wheat disease investigation showed that the relative efficacies of BIO-1 and BIO-2 were up to 82.5% and 83.9%, respectively. Illumina MiSeq sequencing revealed that bacterial abundance and diversity were significantly higher (P < 0.05) in the treatment groups (T1 and T2) than in the control, with significantly decreased fungal diversity in the T2 group. Principal coordinates and hierarchical clustering analyses revealed that the bacterial and fungal communities were distinctly separated between the treatment and control groups. Bacterial community composition analysis demonstrated that beneficial microbes, such as Sphingomonas, Bacillus, Nocardioides, Rhizobium, Streptomyces, Pseudomonas, and Microbacterium, were more abundant in the treatment groups than in the control group. Fungal community composition analysis revealed that the relative abundance of the phytopathogenic fungi Fusarium and Gibberella decreased and that the well-known beneficial fungi Chaetomium, Penicillium, and Humicola were more abundant in the treatment groups than in the control group. Overall, these results confirm that beneficial microbes accumulate more easily in the wheat rhizosphere following application of BIO-1 and BIO-2 and that the relative abundance of phytopathogenic fungi decreased compared with that in the control group.

Degradation of high energetic material hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) by a microbial consortium using response surface methodological approach

Soil and water get polluted with hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) during its manufacturing, storage and use for civil and military purposes. RDX has toxic effects on living and non-living environment and is a recalcitrant compound. Therefore, the remediation of this compound is necessary. Microbial degradation of RDX can be a suitable and sustainable option to reduce its deleterious impact on the environment. Therefore, the optimization for degradation of energetic munition compound RDX employing the consortium of native bacterial species, isolated from an actual contaminated site, was performed. The experiment was planned with three independent variables (initial RDX concentration, inoculum size of microbes, and duration of the experiment) and three dependent variables (percentage removal of RDX, optical density, and nitrite release). Both independent and dependent variables were analyzed by the response surface methodology (RSM) using the Box–Behnken design. The statistical analysis using analysis of variance (ANOVA) depicted a high regression coefficient, R2 = 0.9881 with the statistically significant p-value fitted into a quadratic regression model for percentage removal of RDX. Results showed an initial RDX concentration of 40 mg/L, inoculation size 6 mL and a time duration of 12 days was optimal for the reduction of RDX up to 80.4%.

Revisiting Plant-Microbe Interactions and Microbial Consortia Application for Enhancing Sustainable Agriculture: A Review

The present scenario of agricultural sector is dependent hugely on the use of chemical-based fertilizers and pesticides that impact the nutritional quality, health status, and productivity of the crops. Moreover, continuous release of these chemical inputs causes toxic compounds such as metals to accumulate in the soil and move to the plants with prolonged exposure, which ultimately impact the human health. Hence, it becomes necessary to bring out the alternatives to chemical pesticides/fertilizers for improvement of agricultural outputs. The rhizosphere of plant is an important niche with abundant microorganisms residing in it. They possess the properties of plant growth promotion, disease suppression, removal of toxic compounds, and assimilating nutrients to plants. Utilizing such beneficial microbes for crop productivity presents an efficient way to modulate the crop yield and productivity by maintaining healthy status and quality of the plants through bioformulations. To understand these microbial formulation compositions, it becomes essential to understand the processes going on in the rhizosphere as well as their concrete identification for better utilization of the microbial diversity such as plant growth–promoting bacteria and arbuscular mycorrhizal fungi. Hence, with this background, the present review article highlights the plant microbiome aboveground and belowground, importance of microbial inoculants in various plant species, and their subsequent interactive mechanisms for sustainable agriculture.

Respiratory CO2 Combined With a Blend of Volatiles Emitted by Endophytic Serendipita Strains Strongly Stimulate Growth of Arabidopsis Implicating Auxin and Cytokinin Signaling

Rhizospheric microorganisms can alter plant physiology and morphology in many different ways including through the emission of volatile organic compounds (VOCs). Here we demonstrate that VOCs from beneficial root endophytic Serendipita spp. are able to improve the performance of in vitro grown Arabidopsis seedlings, with an up to 9.3-fold increase in plant biomass. Additional changes in VOC-exposed plants comprised petiole elongation, epidermal cell and leaf area expansion, extension of the lateral root system, enhanced maximum quantum efficiency of photosystem II (Fv/Fm), and accumulation of high levels of anthocyanin. Notwithstanding that the magnitude of the effects was highly dependent on the test system and cultivation medium, the volatile blends of each of the examined strains, including the references S. indica and S. williamsii, exhibited comparable plant growth-promoting activities. By combining different approaches, we provide strong evidence that not only fungal respiratory CO2 accumulating in the headspace, but also other volatile compounds contribute to the observed plant responses. Volatile profiling identified methyl benzoate as the most abundant fungal VOC, released especially by Serendipita cultures that elicit plant growth promotion. However, under our experimental conditions, application of methyl benzoate as a sole volatile did not affect plant performance, suggesting that other compounds are involved or that the mixture of VOCs, rather than single molecules, accounts for the strong plant responses. Using Arabidopsis mutant and reporter lines in some of the major plant hormone signal transduction pathways further revealed the involvement of auxin and cytokinin signaling in Serendipita VOC-induced plant growth modulation. Although we are still far from translating the current knowledge into the implementation of Serendipita VOCs as biofertilizers and phytostimulants, volatile production is a novel mechanism by which sebacinoid fungi can trigger and control biological processes in plants, which might offer opportunities to address agricultural and environmental problems in the future.

Multifaceted applications of isolated microalgae Chlamydomonas sp. TRC-1 in wastewater remediation, lipid production and bioelectricity generation

Green microalga, Chlamydomonas sp. TRC-1 (C. TRC-1), isolated from the outlet of effluent treatment plant of textile dyeing mill, was investigated for its competence towards bioremediation. Algal biomass obtained after remediation (ABAR) was implied for bioelectricity and biofuel production. C. TRC-1 could completely decolorize the effluent in 7 days. Significant reduction in pollution-indicating parameters was observed. Chronoamperometric studies were carried out using cyclic voltammetry and electrochemical impedance spectroscopy (EIS). Maximum current density, power and power density of 3.6 A m^-2, 4.13 × 10^-4 W and 1.83 W m^-2, respectively were generated in ABAR. EIS studies showed a decrease in resistance of ABAR, supporting better electron transfer as compared to algal biomass before remediation (ABBR). Its candidature for biofuel production was assessed by estimating the total lipid content. Results revealed enhancement in lipid content from 46.85% (ABBR) to 79.1% (ABAR). Current study advocates versatile potential of isolated C. TRC-1 for bioremediation of wastewater, bioelectricity production and biofuel generation.

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.

Production and Implication of Bio-Activated Organic Fertilizer Enriched with Zinc-Solubilizing Bacteria to Boost up Maize (Zea mays L.) Production and Biofortification under Two Cropping Seasons

Bio-activated organic fertilizers (BOZ) were produced by enriching the zinc oxide (ZnO)-orange peel waste composite with Zn solubilizing bacteria (ZSB: Bacillus sp. AZ6) in various formulations (BOZ1 (9:1), BOZ2 (8:2), BOZ3 (7:3) and BOZ4 (6:4)). The produced BOZs, along with ZnO, ZnSO4, ZSB were applied to maize crop (Zea mays L.) under field conditions in two different cropping season and the growth, yield, physiology, plant Zn contents and quality of maize were investigated. Results revealed significant variation in the aforementioned parameters with the applied amendments. The BOZ4 performed outclass by exhibiting the highest plant growth, yield, physiology, Zn contents, and quality. On average, an increase of 53%, 49%, 19%, 22%, 10%, 4%, and 30% in plant height was noticed with BOZ4 application over control, ZnO, ZnSO4, BOZ1, BOZ2, BOZ3, and ZSB, respectively. BOZ4 enhanced the dry shoot-biomass 46% than control. Likewise, the photosynthetic rate, transpiration rate, stomatal conductance, chlorophyll contents, carotenoids, and carbonic anhydrase activity were increased by 47%, 42%, 45%, 57%, 17%, and 44%, respectively, under BOZ4 over control in both cropping seasons. However, BOZ4 reduced the electrolyte leakage by 38% as compared to control in both cropping seasons. BOZ4 increased the Zn contents of grain and shoot by 46% and 52%, respectively, while reduced the phytate contents by 73% as compared to control. Application of BOZ4 revealed highest average fat (4.79%), crude protein (12.86%), dry matter (92.03%), fiber (2.87%), gluten (11.925%) and mineral (1.53%) contents, as compared to control. In general, the impact of cropping seasons on maize growth, yield, physiology, Zn contents, and quality were non-significant (with few exceptions). Thus, bio-activation of ZnO with ZSB could serve as an efficient and economical strategy for boosting up the growth, yield, physiological, and quality parameters of maize under field conditions.