The Inherent Conflicts in Developing Soil Microbial Inoculants

Decrease due to pollution in the rhizosphere microbial diversity can be amended by supplementation from adapted plants of another species

Manipulating the rhizosphere microbiome to enhance plant stress tolerance is an environmentally friendly technology and a renewable resource to restore degraded environments. Here we suggest a sustainable bioremediation strategy on the example of Stebnyk mine tailings storage. We consider Salicornia europaea rhizosphere community, and the ability of the phytoremediation plant Salix viminalis to recruit its beneficial microbiome to mediate the pollution stress at the Stebnyk mine tailings storage. The tailings contain large amounts of brine salts and heavy metals that contaminate the ground water and surrounding areas, changing soil biogeochemistry and causing increased erosion. The species richness of the endophytic bacterial community of S. viminalis roots was assessed based on observed OTUs, Shannon-InvSimpson, and evenness index. Our results obtained using the plant-based enrichment strategy show that biodiversity was decreased across the contamination zones and that S. europaea supplementation significantly increased the species richness. Our results also indicate that the number of dominating bacteria was not changed across zones in both S. europaea-treated and untreated bacterial populations, and that the decrease in richness was mainly caused by the low abundant bacterial OTUs. The importance of selecting the bioremediation strains that are likely to harbor a reservoir of genetic traits that aid in bioremediation function from the target environment is discussed.

DNA stable isotope probing reveals the impact of trophic interactions on bioaugmentation of soils with different pollution histories

BACKGROUND

Bioaugmentation is considered a sustainable and cost-effective methodology to recover contaminated environments, but its outcome is highly variable. Predation is a key top-down control mechanism affecting inoculum establishment, however, its effects on this process have received little attention. This study focused on the impact of trophic interactions on bioaugmentation success in two soils with different pollution exposure histories. We inoculated a 13C-labelled pollutant-degrading consortium in these soils and tracked the fate of the labelled biomass through stable isotope probing (SIP) of DNA. We identified active bacterial and eukaryotic inoculum-biomass consumers through amplicon sequencing of 16S rRNA and 18S rRNA genes coupled to a novel enrichment factor calculation.

RESULTS

Inoculation effectively increased PAH removal in the short-term, but not in the long-term polluted soil. A decrease in the relative abundance of the inoculated genera was observed already on day 15 in the long-term polluted soil, while growth of these genera was observed in the short-term polluted soil, indicating establishment of the inoculum. In both soils, eukaryotic genera dominated as early incorporators of 13C-labelled biomass, while bacteria incorporated the labelled biomass at the end of the incubation period, probably through cross-feeding. We also found different successional patterns between the two soils. In the short-term polluted soil, Cercozoa and Fungi genera predominated as early incorporators, whereas Ciliophora, Ochrophyta and Amoebozoa were the predominant genera in the long-term polluted soil.

CONCLUSION

Our results showed differences in the inoculum establishment and predator community responses, affecting bioaugmentation efficiency. This highlights the need to further study predation effects on inoculum survival to increase the applicability of inoculation-based technologies. Video Abstract.

Manipulating geological phosphorus resources for improved production and environmental outcomes during plant establishment

Phosphorus (P) fertilisers are under scrutiny due to resource constraints and environmental impacts. Simple rock phosphate (RP) modifications with acids and co-applied with microbial inoculum could offer sustainable alternative P fertiliser products. We evaluated the effects of acid-treated rock phosphate (RP) in combination with fungal inoculum on plant establishment, environmental impacts (nutrient leaching) and soil quality in a 5-month pot trial. The treatments were evaluated in a clayey Vertisol and a silty Acrisol using cotton (Gossypium hirsutum) as a model plant. The RP treatments - apart from the unmodified and HCl products - were effective in promoting plant establishment with two of the microbial formulations superior to conventional P fertilisers by an average factor of 2 in both soil types (p < 0.05). All RP products restricted P leaching compared with conventional P fertilisers (p < 0.05), by an average factor of 5 for diammonium phosphate (DAP) in both soil types and 3 for the triple superphosphate TSP (only in Acrisol). Nitrate leaching from all treatments was high although much lower from the RP treatments compared with the conventional fertilisers towards the end of the establishment trial, by an average factor of 1.5 (p < 0.05). Ranking analysis revealed that some RP treatments showed evidence for improved ongoing soil quality, including decreased P leaching and soil acidification risks. Microbial analysis showed complex interactions between treatment and soil type. Nonetheless, inoculum persistence at the end of the plant establishment phase was observed for all pots analysed. Our results demonstrate that relatively simple modifications to RP could pave the way for developing sustainable P fertilisers.

Development of a Pseudomonas-based biocontrol consortium with effective root colonization and extended beneficial side effects for plants under high-temperature stress

The root microbiota plays a crucial role in plant performance. The use of microbial consortia is considered a very useful tool for studying microbial interactions in the rhizosphere of different agricultural crop plants. Thus, a consortium of 3 compatible beneficial rhizospheric Pseudomonas strains previously isolated from the avocado rhizosphere, was constructed. The consortium is composed of two compatible biocontrol P. chlororaphis strains (PCL1601 and PCL1606), and the biocontrol rhizobacterium Pseudomonas alcaligenes AVO110, which are all efficient root colonizers of avocado and tomato plants. These three strains were compatible with each other and reached stable levels both in liquid media and on plant roots. Bacterial strains were fluorescent tagged, and colonization-related traits were analyzed in vitro, revealing formation of mixed biofilm networks without exclusion of any of the strains. Additionally, bacterial colonization patterns compatible with the different strains were observed, with high survival traits on avocado and tomato roots. The bacteria composing the consortium shared the same root habitat and exhibited biocontrol activity against soil-borne fungal pathogens at similar levels to those displayed by the individual strains. As expected, because these strains were isolated from avocado roots, this Pseudomonas-based consortium had more stable bacterial counts on avocado roots than on tomato roots; however, inoculation of tomato roots with this consortium was shown to protect tomato plants under high-temperature stress. The results revealed that this consortium has side beneficial effect for tomato plants under high-temperature stress, thus improving the potential performance of the individual strains. We concluded that this rhizobacterial consortium do not improve the plant protection against soil-borne phytopathogenic fungi displayed by the single strains; however, its inoculation can show an specific improvement of plant performance on a horticultural non-host plant (such as tomato) when the plant was challenged by high temperature stress, thus extending the beneficial role of this bacterial consortium.

Practical applications of soil microbiota to improve ecosystem restoration: current knowledge and future directions

Soil microbiota are important components of healthy ecosystems. Greater consideration of soil microbiota in the restoration of biodiverse, functional, and resilient ecosystems is required to address the twin global crises of biodiversity decline and climate change. In this review, we discuss available and emerging practical applications of soil microbiota into (i) restoration planning, (ii) direct interventions for shaping soil biodiversity, and (iii) strategies for monitoring and predicting restoration trajectories. We show how better planning of restoration activities to account for soil microbiota can help improve progress towards restoration targets. We show how planning to embed soil microbiota experiments into restoration projects will permit a more rigorous assessment of the effectiveness of different restoration methods, especially when complemented by statistical modelling approaches that capitalise on existing data sets to improve causal understandings and prioritise research strategies where appropriate. In addition to recovering belowground microbiota, restoration strategies that include soil microbiota can improve the resilience of whole ecosystems. Fundamentally, restoration planning should identify appropriate reference target ecosystem attributes and - from the perspective of soil microbiota - comprehensibly consider potential physical, chemical and biological influences on recovery. We identify that inoculating ecologically appropriate soil microbiota into degraded environments can support a range of restoration interventions (e.g. targeted, broad-spectrum and cultured inoculations) with promising results. Such inoculations however are currently underutilised and knowledge gaps persist surrounding successful establishment in light of community dynamics, including priority effects and community coalescence. We show how the ecological trajectories of restoration sites can be assessed by characterising microbial diversity, composition, and functions in the soil. Ultimately, we highlight practical ways to apply the soil microbiota toolbox across the planning, intervention, and monitoring stages of ecosystem restoration and address persistent open questions at each stage. With continued collaborations between researchers and practitioners to address knowledge gaps, these approaches can improve current restoration practices and ecological outcomes.

Meta-analysis reveals the effects of microbial inoculants on the biomass and diversity of soil microbial communities

Microbial inoculation involves transplanting microorganisms from their natural habitat to new plants or soils to improve plant performance, and it is being increasingly used in agriculture and ecological restoration. However, microbial inoculants can invade and alter the composition of native microbial communities; thus, a comprehensive analysis is urgently needed to understand the overall impact of microbial inoculants on the biomass, diversity, structure and network complexity of native communities. Here we provide a meta-analysis of 335 studies revealing a positive effect of microbial inoculants on soil microbial biomass. This positive effect was weakened by environmental stress and enhanced by the use of fertilizers and native inoculants. Although microbial inoculants did not alter microbial diversity, they induced major changes in the structure and bacterial composition of soil microbial communities, reducing the complexity of bacterial networks and increasing network stability. Finally, higher initial levels of soil nutrients amplified the positive impact of microbial inoculants on fungal biomass, actinobacterial biomass, microbial biomass carbon and microbial biomass nitrogen. Together, our results highlight the positive effects of microbial inoculants on soil microbial biomass, emphasizing the benefits of native inoculants and the important regulatory roles of soil nutrient levels and environmental stress.

Unlocking bacterial potential to reduce farmland N2O emissions

Farmed soils contribute substantially to global warming by emitting N2O (ref. 1), and mitigation has proved difficult2. Several microbial nitrogen transformations produce N2O, but the only biological sink for N2O is the enzyme NosZ, catalysing the reduction of N2O to N2 (ref. 3). Although strengthening the NosZ activity in soils would reduce N2O emissions, such bioengineering of the soil microbiota is considered challenging4,5. However, we have developed a technology to achieve this, using organic waste as a substrate and vector for N2O-respiring bacteria selected for their capacity to thrive in soil6-8. Here we have analysed the biokinetics of N2O reduction by our most promising N2O-respiring bacterium, Cloacibacterium sp. CB-01, its survival in soil and its effect on N2O emissions in field experiments. Fertilization with waste from biogas production, in which CB-01 had grown aerobically to about 6 × 109 cells per millilitre, reduced N2O emissions by 50-95%, depending on soil type. The strong and long-lasting effect of CB-01 is ascribed to its tenacity in soil, rather than its biokinetic parameters, which were inferior to those of other strains of N2O-respiring bacteria. Scaling our data up to the European level, we find that national anthropogenic N2O emissions could be reduced by 5-20%, and more if including other organic wastes. This opens an avenue for cost-effective reduction of N2O emissions for which other mitigation options are lacking at present.

Real-Time PCR (qtPCR) to Discover the Fate of Plant Growth-Promoting Rhizobacteria (PGPR) in Agricultural Soils

To optimize the application of plant growth-promoting rhizobacteria (PGPR) in field trials, tracking methods are needed to assess their shelf life and to determine the elements affecting their effectiveness and their interactions with plants and native soil microbiota. This work developed a real-time PCR (qtPCR) method which traces and quantifies bacteria when added as microbial consortia, including five PGPR species: Burkholderia ambifaria, Bacillus amyloliquefaciens, Azotobacter chroococcum, Pseudomonas fluorescens, and Rahnella aquatilis. Through a literature search and in silico sequence analyses, a set of primer pairs which selectively tag three bacterial species (B. ambifaria, B. amyloliquefaciens and R. aquatilis) was retrieved. The primers were used to trace these microbial species in a field trial in which the consortium was tested as a biostimulant on two wheat varieties, in combination with biochar and the mycorrhizal fungus Rhizophagus intraradices. The qtPCR assay demonstrated that the targeted bacteria had colonized and grown into the soil, reaching a maximum of growth between 15 and 20 days after inoculum. The results also showed biochar had a positive effect on PGPR growth. In conclusion, qtPCR was once more an effective method to trace the fate of supplied bacterial species in the consortium when used as a cargo system for their delivery.

Cooperative interactions between invader and resident microbial community members weaken the negative diversity-invasion relationship

The negative diversity-invasion relationship observed in microbial invasion studies is commonly explained by competition between the invader and resident populations. However, whether this relationship is affected by invader-resident cooperative interactions is unknown. Using ecological and mathematical approaches, we examined the survival and functionality of Aminobacter niigataensis MSH1 to mineralize 2,6-dichlorobenzamide (BAM), a groundwater micropollutant affecting drinking water production, in sand microcosms when inoculated together with synthetic assemblies of resident bacteria. The assemblies varied in richness and in strains that interacted pairwise with MSH1, including cooperative and competitive interactions. While overall, the negative diversity-invasion relationship was retained, residents engaging in cooperative interactions with the invader had a positive impact on MSH1 survival and functionality, highlighting the dependency of invasion success on community composition. No correlation existed between community richness and the delay in BAM mineralization by MSH1. The findings suggest that the presence of cooperative residents can alleviate the negative diversity-invasion relationship.

The role of rhizosphere phages in soil health

While the One Health framework has emphasized the importance of soil microbiomes for plant and human health, one of the most diverse and abundant groups-bacterial viruses, i.e. phages-has been mostly neglected. This perspective reviews the significance of phages for plant health in rhizosphere and explores their ecological and evolutionary impacts on soil ecosystems. We first summarize our current understanding of the diversity and ecological roles of phages in soil microbiomes in terms of nutrient cycling, top-down density regulation, and pathogen suppression. We then consider how phages drive bacterial evolution in soils by promoting horizontal gene transfer, encoding auxiliary metabolic genes that increase host bacterial fitness, and selecting for phage-resistant mutants with altered ecology due to trade-offs with pathogen competitiveness and virulence. Finally, we consider challenges and avenues for phage research in soil ecosystems and how to elucidate the significance of phages for microbial ecology and evolution and soil ecosystem functioning in the future. We conclude that similar to bacteria, phages likely play important roles in connecting different One Health compartments, affecting microbiome diversity and functions in soils. From the applied perspective, phages could offer novel approaches to modulate and optimize microbial and microbe-plant interactions to enhance soil health.

Harnessing rhizospheric core microbiomes from arid regions for enhancing date palm resilience to climate change effects

Date palm cultivation has thrived in the Gulf Cooperation Council region since ancient times, where it represents a vital sector in agricultural and socio-economic development. However, climate change conditions prevailing for decades in this area, next to rarefication of rain, hot temperatures, intense evapotranspiration, rise of sea level, salinization of groundwater, and intensification of cultivation, contributed to increase salinity in the soil as well as in irrigation water and to seriously threaten date palm cultivation sustainability. There are also growing concerns about soil erosion and its repercussions on date palm oases. While several reviews have reported on solutions to sustain date productivity, including genetic selection of suitable cultivars for the local harsh environmental conditions and the implementation of efficient management practices, no systematic review of the desertic plants' below-ground microbial communities and their potential contributions to date palm adaptation to climate change has been reported yet. Indeed, desert microorganisms are expected to address critical agricultural challenges and economic issues. Therefore, the primary objectives of the present critical review are to (1) analyze and synthesize current knowledge and scientific advances on desert plant-associated microorganisms, (2) review and summarize the impacts of their application on date palm, and (3) identify possible gaps and suggest relevant guidance for desert plant microbes' inoculation approach to sustain date palm cultivation within the Gulf Cooperation Council in general and in Qatar in particular.

The interplay between microbial communities and soil properties

In recent years, there has been considerable progress in determining the soil properties that influence the structure of the soil microbiome. By contrast, the effects of microorganisms on their soil habitat have received less attention with most previous studies focusing on microbial contributions to soil carbon and nitrogen dynamics. However, soil microorganisms are not only involved in nutrient cycling and organic matter transformations but also alter the soil habitat through various biochemical and biophysical mechanisms. Such microbially mediated modifications of soil properties can have local impacts on microbiome assembly with pronounced ecological ramifications. In this Review, we describe the processes by which microorganisms modify the soil environment, considering soil physics, hydrology and chemistry. We explore how microorganism-soil interactions can generate feedback loops and discuss how microbially mediated modifications of soil properties can serve as an alternative avenue for the management and manipulation of microbiomes to combat soil threats and global change.

Customized plant microbiome engineering for food security

Plant microbiomes play a vital role in promoting plant growth and resilience to cope with environmental stresses. Plant microbiome engineering holds significant promise to increase crop yields, but there is uncertainty about how this can best be achieved. We propose a step-by-step approach involving customized direct and indirect methods to condition soils and to match plants and microbiomes. Although three approaches, namely the development of (i) 'plant- and microbe-friendly' soils, (ii) 'microbe-friendly' plants, and (iii) 'plant-friendly' microbiomes, have been successfully tested in isolation, we propose that the combination of all three may lead to a step-change towards higher and more stable crop yields. This review aims to provide knowledge, future directions, and practical guidance to achieve this goal via customized plant microbiome engineering.

Rhizosphere engineering for soil carbon sequestration

The rhizosphere is the central hotspot of water and nutrient uptake by plants, rhizodeposition, microbial activities, and plant-soil-microbial interactions. The plasticity of plants offers possibilities to engineer the rhizosphere to mitigate climate change. We define rhizosphere engineering as targeted manipulation of plants, soil, microorganisms, and management to shift rhizosphere processes for specific aims [e.g., carbon (C) sequestration]. The rhizosphere components can be engineered by agronomic, physical, chemical, biological, and genomic approaches. These approaches increase plant productivity with a special focus on C inputs belowground, increase microbial necromass production, protect organic compounds and necromass by aggregation, and decrease C losses. Finally, we outline multifunctional options for rhizosphere engineering: how to boost C sequestration, increase soil health, and mitigate global change effects.

Niche availability and competitive loss by facilitation control proliferation of bacterial strains intended for soil microbiome interventions

Microbiome engineering - the targeted manipulation of microbial communities - is considered a promising strategy to restore ecosystems, but experimental support and mechanistic understanding are required. Here, we show that bacterial inoculants for soil microbiome engineering may fail to establish because they inadvertently facilitate growth of native resident microbiomes. By generating soil microcosms in presence or absence of standardized soil resident communities, we show how different nutrient availabilities limit outgrowth of focal bacterial inoculants (three Pseudomonads), and how this might be improved by adding an artificial, inoculant-selective nutrient niche. Through random paired interaction assays in agarose micro-beads, we demonstrate that, in addition to direct competition, inoculants lose competitiveness by facilitating growth of resident soil bacteria. Metatranscriptomics experiments with toluene as selective nutrient niche for the inoculant Pseudomonas veronii indicate that this facilitation is due to loss and uptake of excreted metabolites by resident taxa. Generation of selective nutrient niches for inoculants may help to favor their proliferation for the duration of their intended action while limiting their competitive loss.

Seedling microbiota engineering using bacterial synthetic community inoculation on seeds

Synthetic Communities (SynComs) are being developed and tested to manipulate plant microbiota and improve plant health. To date, only few studies proposed the use of SynCom on seed despite its potential for plant microbiota engineering. We developed and presented a simple and effective seedling microbiota engineering method using SynCom inoculation on seeds. The method was successful using a wide diversity of SynCom compositions and bacterial strains that are representative of the common bean seed microbiota. First, this method enables the modulation of seed microbiota composition and community size. Then, SynComs strongly outcompeted native seed and potting soil microbiota and contributed on average to 80% of the seedling microbiota. We showed that strain abundance on seed was a main driver of an effective seedling microbiota colonization. Also, selection was partly involved in seed and seedling colonization capacities since strains affiliated to Enterobacteriaceae and Erwiniaceae were good colonizers while Bacillaceae and Microbacteriaceae were poor colonizers. Additionally, the engineered seed microbiota modified the recruitment and assembly of seedling and rhizosphere microbiota through priority effects. This study shows that SynCom inoculation on seeds represents a promising approach to study plant microbiota assembly and its consequence on plant fitness.

Bacillus species as tools for biocontrol of plant diseases: A meta-analysis of twenty-two years of research, 2000-2021

The traditional way of dealing with plant diseases has been the use of chemical products, but these harm the environment and are incompatible with the global effort for sustainable development. The use of Bacillus and related species in the biological control of plant diseases is a trend in green agriculture. Many studies report the positive effect of these bacteria, but a synthesis is still necessary. So, the objective of this work is to perform a meta-analysis of Bacillus biocontrol potential and identify factors that drive its efficacy. Data were compiled from articles published in journals listed in two of the main scientific databases between 2000 and 2021. Among 6159 articles retrieved, 399 research papers met the inclusion criteria for a systematic review. Overall, Bacilli biocontrol agents reduced disease by 60% compared to control groups. Furthermore, experimental tests with higher concentrations show a strong protective effect, unlike low and single concentration essays. Biocontrol efficacy also increased when used as a protective inoculation rather than therapeutic inoculation. Inoculation directly in the fruit has a greater effect than soil drenching. The size of the effect of Bacillus-based commercial products is lower than the newly tested strains. The findings presented in this study confirm the power of Bacillus-based bioinoculants and provide valuable guidance for practitioners, researchers, and policymakers seeking effective and sustainable solutions in plant disease management.

Survival of a microbial inoculant in soil after recurrent inoculations

Microbial inoculants are attracting growing interest in agriculture, but their efficacy remains unreliable in relation to their poor survival, partly due to the competition with the soil resident community. We hypothesised that recurrent inoculation could gradually alleviate this competition and improve the survival of the inoculant while increasing its impact on the resident bacterial community. We tested the effectiveness of such strategy with four inoculation sequences of Pseudomonas fluorescens strain B177 in soil microcosms with increasing number and frequency of inoculation, compared to a non-inoculated control. Each sequence was carried out at two inoculation densities (106 and 108 cfu.g soil-1). The four-inoculation sequence induced a higher abundance of P. fluorescens, 2 weeks after the last inoculation. No impact of inoculation sequences was observed on the resident community diversity and composition. Differential abundance analysis identified only 28 out of 576 dominants OTUs affected by the high-density inoculum, whatever the inoculation sequence. Recurrent inoculations induced a strong accumulation of nitrate, not explained by the abundance of nitrifying or nitrate-reducing microorganisms. In summary, inoculant density rather than inoculation pattern matters for inoculation effect on the resident bacterial communities, while recurrent inoculation allowed to slightly enhance the survival of the inoculant and strongly increased soil nitrate content.

Evolutionary consequences of microbiomes for hosts: impacts on host fitness, traits, and heritability

An organism's phenotypes and fitness often depend on the interactive effects of its genome (Gh⁢o⁢s⁢t), microbiome (Gm⁢i⁢c⁢r⁢o⁢b⁢e), and environment (E). These G × G, G × E, and G × G × E effects fundamentally shape host-microbiome (co)evolution and may be widespread, but are rarely compared within a single experiment. We collected and cultured L⁢e⁢m⁢n⁢am⁢i⁢n⁢o⁢r (duckweed) and its associated microbiome from 10 sites across an urban-to-rural ecotone. We factorially manipulated host genotype and microbiome in two environments (low and high zinc, an urban aquatic stressor) in an experiment with 200 treatments: 10 host genotypes × 10 microbiomes × 2 environments. Host genotype explained the most variation in L.m⁢i⁢n⁢o⁢r fitness and traits, while microbiome effects often depended on host genotype (G × G). Microbiome composition predicted G × G effects: when compared in more similar microbiomes, duckweed genotypes had more similar effects on traits. Further, host fitness increased and microbes grew faster when applied microbiomes more closely matched the host's field microbiome, suggesting some local adaptation between hosts and microbiota. Finally, selection on and heritability of host traits shifted across microbiomes and zinc exposure. Thus, we found that microbiomes impact host fitness, trait expression, and heritability, with implications for host-microbiome evolution and microbiome breeding.

Soil microbiome analysis supports claims of ineffectiveness of Pseudomonas fluorescens D7 as a biocontrol agent of Bromus tectorum

IMPORTANCE

Cheatgrass is one of North America's most problematic invasive species. Invasion by this annual grass alters ecosystem structure and function and has proven very challenging to remove with traditional approaches. Commercially available bioherbicides, like P. fluorescens D7, are applied with the goal of providing lasting control from a single application. However, experimental results suggest that this bioherbicide has limited efficacy under field conditions. Potential explanations for variable efficacy include a failure of this bioherbicide to establish in the soil microbiome. However, to our knowledge, no data exist to support or refute this hypothesis. Here, we use a deep-sequencing approach to better understand the effects of this bioherbicide on the soil microbiome and screen for P. fluorescens at 18 months post-application.

Leveraging aquatic-terrestrial interfaces to capture putative habitat generalists

Habitat type is a strong determinant of microbial composition. Habitat interfaces, such as the boundary between aquatic and terrestrial systems, present unique combinations of abiotic factors for microorganisms to contend with. Aside from the spillover of certain harmful microorganisms from agricultural soils into water (e.g. fecal coliform bacteria), we know little about the extent of soil-water habitat switching across microbial taxa. In this study, we developed a proof-of-concept system to facilitate the capture of putatively generalist microorganisms that can colonize and persist in both soil and river water. We aimed to examine the phylogenetic breadth of putative habitat switchers and how this varies across different source environments. Microbial composition was primarily driven by recipient environment type, with the strongest phylogenetic signal seen at the order level for river water colonizers. We also identified more microorganisms colonizing river water when soil was collected from a habitat interface (i.e. soil at the side of an intermittently flooded river, compared to soil collected further from water sources), suggesting that environmental interfaces could be important reservoirs of microbial habitat generalists. Continued development of experimental systems that actively capture microorganisms that thrive in divergent habitats could serve as a powerful tool for identifying and assessing the ecological distribution of microbial generalists.

The biocontrol agent Lactiplantibacillus plantarum AMBP214 is dispersible to plants via bumblebees

IMPORTANCE

Plant protection products are essential for ensuring food production, but their use poses a threat to human and environmental health, and their efficacy is decreasing due to the acquisition of resistance by pathogens. Stricter regulations and consumer demand for cleaner produce are driving the search for safer and more sustainable alternatives. Microbial biocontrol agents, such as microorganisms with antifungal activity, have emerged as a promising alternative management strategy, but their commercial use has been limited by poor establishment and spread on crops. This study presents a novel system to overcome these challenges. The biocontrol agent Lactiplantibacillus plantarum AMBP214 was spray-dried and successfully dispersed to strawberry flowers via bumblebees. This is the first report of combining spray-dried, non-spore-forming bacteria with pollinator-dispersal, which scored better than the state-of-the-art in terms of dispersal to the plant (CFU/flower), and resuscitation of the biocontrol agent. Therefore, this new entomovectoring system holds great promise for the use of biocontrol agents for disease management in agriculture.

Plant Growth-Promoting Bacteria of Soil: Designing of Consortia Beneficial for Crop Production

Plant growth-promoting bacteria are commonly used in agriculture, particularly for seed inoculation. Multispecies consortia are believed to be the most promising form of these bacteria. However, designing and modeling bacterial consortia to achieve desired phenotypic outcomes in plants is challenging. This review aims to address this challenge by exploring key antimicrobial interactions. Special attention is given to approaches for developing soil plant growth-promoting bacteria consortia. Additionally, advanced omics-based methods are analyzed that allow soil microbiomes to be characterized, providing an understanding of the molecular and functional aspects of these microbial communities. A comprehensive discussion explores the utilization of bacterial preparations in biofertilizers for agricultural applications, focusing on the intricate design of synthetic bacterial consortia with these preparations. Overall, the review provides valuable insights and strategies for intentionally designing bacterial consortia to enhance plant growth and development.

Streptomyces as a promising biological control agents for plant pathogens

Plant diseases caused by pathogenic microorganisms in agriculture present a considerable obstacle, resulting in approximately 30-40% crop damage. The use of conventional techniques to manage these microorganisms, i.e., applying chemical pesticides and antimicrobials, has been discovered to have adverse effects on human health and the environment. Furthermore, these methods have contributed to the emergence of resistance among phytopathogens. Consequently, it has become imperative to investigate natural alternatives to address this issue. The Streptomyces genus of gram-positive bacteria is a potentially viable natural alternative that has been extensively researched due to its capacity to generate diverse antimicrobial compounds, such as metabolites and organic compounds. Scientists globally use diverse approaches and methodologies to extract new bioactive compounds from these bacteria. The efficacy of bioactive compounds in mitigating various phytopathogens that pose a significant threat to crops and plants has been demonstrated. Hence, the Streptomyces genus exhibits potential as a biological control agent for combating plant pathogens. This review article aims to provide further insight into the Streptomyces genus as a source of antimicrobial compounds that can potentially be a biological control against plant pathogens. The investigation of various bioactive compounds synthesized by this genus can enhance our comprehension of their prospective utilization in agriculture.

Sugarcane mill mud-induced putative host (soybean (Glycine max))-rhizobia symbiosis in sandy loam soil

Domestic production of controlled-release, compost-based, and microbe-enhanced fertilizers is being expanded in the U.S. as a part of rural development. Sugarcane mill mud is a sterilized (≈90°C) agricultural byproduct in surplus that has received interests as a soil amendment in several Southern states, because of its high phosphorus and organic carbon contents. Addition of mill mud to sandy loam significantly increased the nodule formation compared to fertilized and unfertilized controls. Mill mud addition also resulted in pod yields similar to the fertilized control. Though not found in mill mud itself, mill mud additions correlated with an increase in soil Rhizobia as determined by deep 16S rRNA gene sequencing. We hypothesize that Firmicutes in sterilized mill mud induced Rhizobia that in turn enhanced soybean (Glycine max) growth. Collectively, mill mud enhanced the plant growth promoting bacteria when applied to a silt loam, although the relative influence of mill mud-derived bacteria, organic carbon, and nutrients is yet to be determined.

Bioinoculants as a means of increasing crop tolerance to drought and phosphorus deficiency in legume-cereal intercropping systems

Ensuring plant resilience to drought and phosphorus (P) stresses is crucial to support global food security. The phytobiome, shaped by selective pressures, harbors stress-adapted microorganisms that confer host benefits like enhanced growth and stress tolerance. Intercropping systems also offer benefits through facilitative interactions, improving plant growth in water- and P-deficient soils. Application of microbial consortia can boost the benefits of intercropping, although questions remain about the establishment, persistence, and legacy effects within resident soil microbiomes. Understanding microbe- and plant-microbe dynamics in drought-prone soils is key. This review highlights the beneficial effects of rhizobacterial consortia-based inoculants in legume-cereal intercropping systems, discusses challenges, proposes a roadmap for development of P-solubilizing drought-adapted consortia, and identifies research gaps in crop-microbe interactions.

Microbiome engineering optimized by Antarctic microbiota to support a plant host under water deficit

Climate change challenges modern agriculture to develop alternative and eco-friendly solutions to alleviate abiotic and/or biotic stresses. The use of soil microbiomes from extreme environments opens new avenues to discover novel microorganisms and microbial functions to protect plants. In this study we confirm the ability of a bioinoculant, generated by natural engineering, to promote host development under water stress. Microbiome engineering was mediated through three factors i) Antarctic soil donation, ii) water deficit and iii) multigenerational tomato host selection. We revealed that tomato plants growing in soils supplemented with Antarctic microbiota were tolerant to water deficit stress after 10 generations. A clear increase in tomato seedling tolerance against water deficit stress was observed in all soils over generations of Host Mediated Microbiome Engineering, being Fildes mixture the most representatives, which was evidenced by an increased survival time, plant stress index, biomass accumulation, and decreased leaf proline content. Microbial community analysis using 16s rRNA gene amplicon sequencing data suggested a microbiome restructuring that could be associated with increased tolerance of water deficit. Additionally, the results showed a significant increase in the relative abundance of Candidatus Nitrosocosmicus and Bacillus spp. which could be key taxa associated with the observed tolerance improvement. We proposed that in situ microbiota engineering through the evolution of three factors (long-standing extreme climate adaption and host and stress selection) could represent a promising strategy for novel generation of microbial inoculants.

The phytomicrobiome: solving plant stress tolerance under climate change

With extraordinary global climate changes, increased episodes of extreme conditions result in continuous but complex interaction of environmental variables with plant life. Exploring natural phytomicrobiome species can provide a crucial resource of beneficial microbes that can improve plant growth and productivity through nutrient uptake, secondary metabolite production, and resistance against pathogenicity and abiotic stresses. The phytomicrobiome composition, diversity, and function strongly depend on the plant's genotype and climatic conditions. Currently, most studies have focused on elucidating microbial community abundance and diversity in the phytomicrobiome, covering bacterial communities. However, least is known about understanding the holistic phytomicrobiome composition and how they interact and function in stress conditions. This review identifies several gaps and essential questions that could enhance understanding of the complex interaction of microbiome, plant, and climate change. Utilizing eco-friendly approaches of naturally occurring synthetic microbial communities that enhance plant stress tolerance and leave fewer carbon-foot prints has been emphasized. However, understanding the mechanisms involved in stress signaling and responses by phytomicrobiome species under spatial and temporal climate changes is extremely important. Furthermore, the bacterial and fungal biome have been studied extensively, but the holistic interactome with archaea, viruses, oomycetes, protozoa, algae, and nematodes has seldom been studied. The inter-kingdom diversity, function, and potential role in improving environmental stress responses of plants are considerably important. In addition, much remains to be understood across organismal and ecosystem-level responses under dynamic and complex climate change conditions.

Bacterial inoculation of Quercus pyrenaica trees alters co-occurrence patterns but not the composition of the rhizosphere bacteriome in wild conditions

Quercus pyrenaica is a woody species of high landscape value, however, its forests show an advanced state of degradation in the Iberian Peninsula. Afforestation typically has low success, thus, it is necessary to improve the fitness of oaks plantlets to be transplanted, for instance, by inoculating beneficial microorganisms. In adding microorganisms to ecosystems, there must be balanced efficacy with potential effects on native microbial communities. We addressed changes in diversity, richness, composition and co-occurrence networks of prokaryotic communities in the rhizosphere of inoculated and control trees outplanted to three different sites located in the Sierra Nevada National and Natural Park (Spain). After 18 months in wild conditions, we did not detect changes due to the inoculation in the richness, diversity and structure in none of the sites. However, we observed an increase in the complexity of the co-occurrence networks in two experimental areas. Modularization of the networks changed as a result of the inoculation, although the sense of the change depended on the site. Although it was impossible to unravel the effect of bacterial inoculation, our results highlighted that inoculation alters the association of rhizosphere bacteria without entailing other changes, so networks should be analysed prior to inoculating the plantlets.

Inoculation with thermophiles enhanced the food waste bio-drying and complicated interdomain ecological networks between bacterial and fungal communities

Bio-drying is a practical approach for treating food waste (FW). However, microbial ecological processes during treatment are essential for improving the dry efficiency, and have not been stressed enough. This study analyzed the microbial community succession and two critical periods of interdomain ecological networks (IDENs) during FW bio-drying inoculated with thermophiles (TB), to determine how TB affects FW bio-drying efficiency. The results showed that TB could rapidly colonize in the FW bio-drying, with the highest relative abundance of 5.13%. Inoculating TB increased the maximum temperature, temperature integrated index and moisture removal rate of FW bio-drying (55.7 °C, 219.5 °C, and 86.11% vs. 52.1 °C, 159.1 °C, and 56.02%), thereby accelerating the FW bio-drying efficiency by altering the succession of microbial communities. The structural equation model and IDEN analysis demonstrated that TB inoculation complicated the IDENs between bacterial and fungal communities by significantly and positively affecting bacterial communities (b = 0.39, p < 0.001) and fungal communities (b = 0.32, p < 0.01), thereby enhancing interdomain interactions between bacteria and fungi. Additionally, inoculation TB significantly increased the relative abundance of keystone taxa, including Clostridium sensu stricto, Ochrobactrum, Phenylobacterium, Microvirga and Candida. In conclusion, the inoculation of TB could effectively improve FW bio-drying, which is a promising technology for rapidly reducing FW with high moisture content and recovering resources from it.

A multi-attribute approach to evaluating the impact of biostimulants on crop performance

An ever-growing collection of commercial biostimulants is becoming available in a wide variety of forms and compositions to improve crop performance. Given the intricate nature of deciphering the underlying mechanisms of commercial products, which typically comprise various biological components, it is crucial for research in this area to have robust tools to demonstrate their effectiveness in field trials. Here, we took a multi-attribute approach to evaluating the impact of biostimulants on crop performance. First, we assessed the impact of a biostimulant on the soil and rhizosphere microbiomes associated to crops in eight reference farms, including corn (3 farms), soybean (2), cotton (2) and sugarcane (1), in different biomes and production contexts in Brazil and Paraguay. Second, we modeled a set of integrated indicators to measure crop responses to biostimulant application, including five analytical themes as follows: i) crop development and production (9 indicators), ii) soil chemistry (9), iii) soil physics (5), iv) soil biology (6) and v) plant health (10). Amplicon 16S rRNA and ITS sequencing revealed that the use of the biostimulant consistently changes the structure of bacterial and fungal communities associated with the production system for all evaluated crops. In the rhizosphere samples, the most responsive bacterial taxa to biostimulant application were Prevotella in cotton; Prauserella and Methylovirgula in corn; and Methylocapsa in sugar cane. The most responsive fungal taxa to biostimulant use were Arachnomyces in soybean and cotton; and Rhizophlyctis in corn. The proposed integrated indicators yielded highly favorable positive impact indices (averaging at 0.80), indicating that biostimulant-treated fields correlate with better plant development and crop performance. Prominent indices were observed for indicators in four themes: soil biology (average index 0.84), crop production (0.81), soil physics (compaction reduction 0.81), and chemical fertility (0.75). The multi-attribute approach employed in this study offers an effective strategy for assessing the efficacy of biostimulant products across a wide range of crops and production systems.

Toxic response of antimony in the Comamonas testosteroni and its application in soil antimony bioremediation

Antimony (Sb) is toxic to ecosystems and potentially to public health via its accumulation in the food chain. Bioavailability and toxicity of Sb have been reduced using various methods for the remediation of Sb-contaminated soil in most studies. However, Sb-contaminated soil remediation by microbial agents has been rarely evaluated. In this study, we evaluated the potential for the use of Comamonas testosteroni JL40 in the bioremediation of Sb-contamination. Strain JL40 immobilized more than 30 % of the Sb(III) in solution and oxidized over 18 % to Sb(V) for detoxification. Meanwhile, strain JL40 responds to Sb toxicity through such as Sb efflux, intracellular accumulation, biofilm production, and scavenging of reactive oxygen species (ROS), etc. The results of the pot experiment showed the average Sb content of the brown rice was decreased by 59.1%, 38.8%, and 48.4%, for 1.8, 50, and 100 mg/kg Sb spiked soils, respectively. In addition, the results of plant, soil enzyme activity, and rice agronomic trait observations showed that the application of strain JL40 could maintain the health of plants and soil and improve rice production. The single-step and sequential extraction of Sb from rhizosphere soil showed that strain JL40 also plays a role in Sb immobilization and oxidation in the soil environment. During rice potted cultivation, bacterial community analysis and plate counting showed that the strain JL40 could still maintain 103 CFU/g after 30 days of inoculation. With phenotypic and differential proteomics analysis, strain JL40 conferred Sb(III) tolerance by a combination of immobilization, oxidation, efflux and scavenging of ROS, etc. Our study demonstrates the application of Sb-immobilizing and oxidizing bacteria to lower soil Sb and reduce accumulation of Sb in rice. Our results provide guidance for bacterial remediation of Sb-contaminated soil.

Repeated inoculation of antimony resistant bacterium reduces antimony accumulation in rice plants

Applying beneficial bacteria in rice rhizosphere to manage heavy metal behaviour in soil-plant system is a promising strategy. However, colonization/domination of exogenous bacteria in rhizosphere soils remains a challenge. In this study, a bacterium Ochrobactrum anthropi, which showed the potential of transforming soluble Sb^III into Sb₂O₃ mineral, was repeatedly inoculated into the rice rhizosphere weekly throughout the rice growth period, and the colonization of this bacterium in rice rhizosphere soils and its effect on Sb accumulation in rice plants were investigated. Results showed that repeated inoculants changed the native bacterial community in rhizosphere soils in comparison with the control, but the inoculated O. anthropi was not identified as an abundant species. With weekly inoculation, the decrease in Sb in rice roots and straws was maintained throughout the rice growth period, with decrease percentages ranging from 36 to 49% and 33-35%. In addition, decrease percentages of Sb in husks and grains at the maturing stage obtained 34 and 37%, respectively. Furthermore, the XRD identified the formation of valentinite (Sb₂O₃) on rice root in inoculation treatment, and the decrease percentages in aqueous Sb^III in rhizosphere were 53-100% through the growth period. It demonstrated that weekly inoculants performed their temporary activity of valentinite formation, and reduced Sb accumulation in rice plants efficiently. This study suggests that regardless of successful colonization, repeated inoculation of beneficial bacteria is an option to facilitate the positive effects of inoculated bacteria in the management of heavy metal behaviour.

Role of microbial inoculants as bio fertilizers for improving crop productivity: A review

The world's population is increasing and is anticipated to spread 10 billion by 2050, and the issue of food security is becoming a global concern. To maintain global food security, it is essential to increase crop productivity under changing climatic conditions. Conventional agricultural practices frequently use artificial/chemical fertilizers to enhance crop productivity, but these have numerous negative effects on the environment and people's health. To address these issues, researchers have been concentrating on substitute crop fertilization methods for many years, and biofertilizers as a crucial part of agricultural practices are quickly gaining popularity all over the globe. Biofertilizers are living formulations made of indigenous plant growth-promoting rhizobacteria (PGPR) which are substantial, environment-friendly, and economical biofertilizers for amassing crop productivity by enhancing plant development either directly or indirectly, and are the renewable source of plant nutrients and sustainable agronomy. The review aims to provide a comprehensive overview of the current knowledge on microbial inoculants as biofertilizers, including their types, mechanisms of action, effects on crop productivity, challenges, and limitations associated with the use of microbial inoculants. In this review, we focused on the application of biofertilizers to agricultural fields in plant growth development by performing several activities like nitrogen fixation, siderophore production, phytohormone production, nutrient solubilization, and facilitating easy uptake by crop plants. Further, we discussed the indirect mechanism of PGPRs, in developing induced system resistance against pest and diseases, and as a biocontrol agent for phytopathogens. This review article presents a brief outline of the ideas and uses of microbial inoculants in improving crop productivity as well as a discussion of the challenges and limitations to use microbial inoculants.

The potential for plant growth-promoting bacteria to impact crop productivity in future agricultural systems is linked to understanding the principles of microbial ecology

Global climate change poses challenges to land use worldwide, and we need to reconsider agricultural practices. While it is generally accepted that biodiversity can be used as a biomarker for healthy agroecosystems, we must specify what specifically composes a healthy microbiome. Therefore, understanding how holobionts function in native, harsh, and wild habitats and how rhizobacteria mediate plant and ecosystem biodiversity in the systems enables us to identify key factors for plant fitness. A systems approach to engineering microbial communities by connecting host phenotype adaptive traits would help us understand the increased fitness of holobionts supported by genetic diversity. Identification of genetic loci controlling the interaction of beneficial microbiomes will allow the integration of genomic design into crop breeding programs. Bacteria beneficial to plants have traditionally been conceived as "promoting and regulating plant growth". The future perspective for agroecosystems should be that microbiomes, via multiple cascades, define plant phenotypes and provide genetic variability for agroecosystems.

Home-based microbial solution to boost crop growth in low-fertility soil

Soil microbial inoculants are expected to boost crop productivity under climate change and soil degradation. However, the efficiency of native vs commercialized microbial inoculants in soils with different fertility and impacts on resident microbial communities remain unclear. We investigated the differential plant growth responses to native synthetic microbial community (SynCom) and commercial plant growth-promoting rhizobacteria (PGPR). We quantified the microbial colonization and dynamic of niche structure to emphasize the home-field advantages for native microbial inoculants. A native SynCom of 21 bacterial strains, originating from three typical agricultural soils, conferred a special advantage in promoting maize growth under low-fertility conditions. The root : shoot ratio of fresh weight increased by 78-121% with SynCom but only 23-86% with PGPRs. This phenotype correlated with the potential robust colonization of SynCom and positive interactions with the resident community. Niche breadth analysis revealed that SynCom inoculation induced a neutral disturbance to the niche structure. However, even PGPRs failed to colonize the natural soil, they decreased niche breadth and increased niche overlap by 59.2-62.4%, exacerbating competition. These results suggest that the home-field advantage of native microbes may serve as a basis for engineering crop microbiomes to support food production in widely distributed poor soils.

Drivers of stability and transience in composition-functioning links during serial propagation of litter-decomposing microbial communities

Biotic factors that influence the temporal stability of microbial community functioning are an emerging research focus for control of natural and engineered systems. Discovery of common features within community ensembles that differ in functional stability over time is a starting point to explore biotic factors. We serially propagated a suite of soil microbial communities through five generations of 28 d microcosm incubations to examine microbial community compositional and functional stability during plant-litter decomposition. Using DOC abundance as a target function, we hypothesized that microbial diversity, compositional stability, and associated changes in interactions would explain the relative stability of the ecosystem function between generations. Communities with initially high DOC abundance tended to converge towards a "low DOC" phenotype within two generations, but across all microcosms, functional stability between generations was highly variable. By splitting communities into two cohorts based on their relative DOC functional stability, we found that compositional shifts, diversity, and interaction network complexity were associated with the stability of DOC abundance between generations. Further, our results showed that legacy effects were important in determining compositional and functional outcomes, and we identified taxa associated with high DOC abundance. In the context of litter decomposition, achieving functionally stable communities is required to utilize soil microbiomes to increase DOC abundance and long-term terrestrial DOC sequestration as 1 solution to reduce atmospheric carbon dioxide concentrations. Identifying factors that stabilize function for a community of interest may improve the success of microbiome engineering applications. Importance Microbial community functioning can be highly dynamic over time. Identifying and understanding biotic factors that control functional stability is of significant interest for natural and engineered communities alike. Using plant litter decomposing communities as a model system, this study examined the stability of ecosystem function over time following repeated community transfers. By identifying microbial community features that are associated with stable ecosystem functions, microbial communities can be manipulated in ways that promote the consistency and reliability of the desired function, improving outcomes and increasing the utility of microorganisms.

Selenium and Bacillus proteolyticus SES synergistically enhanced ryegrass to remediate Cu-Cd-Cr contaminated soil

Heavy metal compound contaminated soil is an ecological threat, and soil containing copper (Cu), cadmium (Cd) and chromium (Cr) simultaneously is widely distributed. The application of phytoremediation in heavy metal combined contamination is still limited. In this study, to explore whether and how exogenous selenium (Se) and Bacillus proteolyticus SES enhance the remediation of combined Cu-Cd-Cr contaminated soil by ryegrass, pot experiments were carried out. Se alone or in combination with B. proteolyticus SES treatment increased the removal rates of heavy metals in the rhizosphere soil by 17.38%-157.25% relative to the control, while Se + B. proteolyticus SES treatment played a greater role in improving the heavy metals tolerance of ryegrass and increasing the activity of soil acid phosphatase. Moreover, Se and B. proteolyticus SES favored the preferential recruitment of specific taxa with the capacity of plant growth promotion and heavy metals resistance to the rhizosphere. The rhizosphere soil of Se treatment was specifically enriched with Lysobacter, Rhodanobacter, Micrococcales, Paenarthrobacter, and Adhaeribacter, while from class Bacilli to genus Bacillus enriched extensively and specifically in the rhizosphere of B. proteolyticus SES + Se treatment. Furthermore, five functional beneficial rhizosphere microbes including: Microbacterium sp., Pseudomonas extremaustralis, Bacillus amyloliquefaciens, Priestia megaterium, and Bacillus subtilis were isolated from the two treatments with the best remediation effect and synthetic communities (SynComs) were constructed. SynComs inoculation experiment further demonstrated the role of specific beneficial microbes in regulating the bioavailability of heavy metals. Results revealed that Se supplementation efficiently facilitated the phytoextraction of combined Cu-Cd-Cr contaminated soil, and B. proteolyticus SES inoculation showed the synergistical enhancement effect in the presence of Se.

Phosphate-solubilizing microorganisms regulate the release and transformation of phosphorus in biochar-based slow-release fertilizer

Coupling phosphate-solubilizing microorganisms (PSM) can improve the availability of phosphorous (P) in biochar-based slow-release P fertilizers (BPF). However, the mechanism in release and transformation of P in BPF regulated by PSM is still unclear. Herein, the biocompatibility and the adhesion behaviors of BPF and PSM (Enterobacter hormaechei Rs-198) in soil were firstly studied, and a 90 days' laboratory-scale soil incubation experiment of BPF and Rs-198 was performed to study the transformation of P of BPF. The results show that BPF has a good biocompatibility for Rs-198 due to its low aromaticity, graphitization and free radicals' content (0.084 mg/g). Rs-198 are adhered to the surface of BPF in soil due to the high negative secondary energy minimum and low total interaction energy between Rs-198 and BPF. Available P in the incubation of BPF and Rs-198 (BR treatment) is significantly higher than that of the incubation of BPF (BF treatment) at initial 60 days. However, the content of available P in BR treatment is much lower compared with that in BF treatment on day 90, which is attributed to the entrapment of released P from BPF by Rs-198 and the formation of polyphosphate (polyP) rather than bound with soil mineral. Overall, this study presents new insights into the transformation of P in BPF regulated by PSM.

Effects of sublethal stress application on the survival of bacterial inoculants: a systematic review

The use of commercial bacterial inoculants formulated with plant-growth promoting bacteria (PGPB) in agriculture has shown significant prominence in recent years due to growth-promotion benefits provided to plants through different mechanisms. However, the survival and viability of bacterial cells in inoculants are affected during use and may decrease their effectiveness. Physiological adaptation strategies have attracted attention to solve the viability problem. This review aims to provide an overview of research on selecting sublethal stress strategies to increase the effectiveness of bacterial inoculants. The searches were performed in November 2021 using Web of Science, Scopus, PubMed, and Proquest databases. The keywords "nitrogen-fixing bacteria", "plant growth-promoting rhizobacteria", "azospirillum", "pseudomonas", "rhizobium", "stress pre-conditioning", "adaptation", "metabolic physiological adaptation", "cellular adaptation", "increasing survival", "protective agent" and "protective strategy" were used in the searches. A total of 2573 publications were found, and 34 studies were selected for a deeper study of the subject. Based on the studies analysis, gaps and potential applications related to sublethal stress were identified. The most used strategies included osmotic, thermal, oxidative, and nutritional stress, and the primary cell response mechanism to stress was the accumulation of osmolytes, phytohormones, and exopolysaccharides (EPS). Under sublethal stress, the inoculant survival showed positive increments after lyophilization, desiccation, and long-term storage processes. The effectiveness of inoculant-plants interaction also had positive increments after sublethal stress, improving plant development, disease control, and tolerance to environmental stresses compared to unappealed inoculants.

Drivers of stability and transience in composition-functioning links during serial propagation of litter-decomposing microbial communities

IMPORTANCE

Microbial community functioning can be highly dynamic over time. Identifying and understanding biotic factors that control functional stability is of significant interest for natural and engineered communities alike. Using plant litter decomposing communities as a model system, this study examined the stability of ecosystem function over time following repeated community transfers. By identifying microbial community features that are associated with stable ecosystem functions, microbial communities can be manipulated in ways that promote the consistency and reliability of the desired function, improving outcomes and increasing the utility of microorganisms.

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.

Microalgae as next generation plant growth additives: Functions, applications, challenges and circular bioeconomy based solutions

Sustainable agriculture practices involve the application of environment-friendly plant growth promoters and additives that do not negatively impact the health of the ecosystem. Stringent regulatory frameworks restricting the use of synthetic agrochemicals and the increase in demand for organically grown crops have paved the way for the development of novel bio-based plant growth promoters. In this context, microalgae biomass and derived agrochemicals offer novel sources of plant growth promotors that enhance crop productivity and impart disease resistance. These beneficial effects could be attributed to the presence of wide range of biomolecules such as soluble amino acid (AA), micronutrients, polysaccharides, phytohormones and other signaling molecules in microalgae biomass. In addition, their phototrophic nature, high photosynthetic efficiency, and wide environmental adaptability make them an attractive source of biostimulants, biofertilizers and biopesticides. The present review aims to describe the various plant growth promoting metabolites produced by microalgae and their effects on plant growth and productivity. Further, the effects elicited by microalgae biostimulants with respect to different modes of applications such as seed treatments, foliar spray and soil/root drenching is reviewed in detail. In addition, the ability of microalgae metabolites to impart tolerance against various abiotic and biotic stressors along with the mechanism of action is discussed in this paper. Although the use of microalgae based biofertilizers and biostimulants is gaining popularity, the high nutrient and water requirements and energy intensive downstream processes makes microalgae based technology commercially unsustainable. Addressing this challenge, we propose a circular economy model of microalgae mediated bioremediation coupled with biorefinery approaches of generating high value metabolites along with biofertilizer applications. We discuss and review new trends in enhancing the sustainability of microalgae biomass production by co-cultivation of algae with hydroponics and utilization of agriculture effluents.

Microbial Drivers of Plant Performance during Drought Depend upon Community Composition and the Greater Soil Environment

The increasing occurrence of drought is a global challenge that threatens food security through direct impacts to both plants and their interacting soil microorganisms. Plant growth promoting microbes are increasingly being harnessed to improve plant performance under stress. However, the magnitude of microbiome impacts on both structural and physiological plant traits under water limited and water replete conditions are not well-characterized. Using two microbiomes sourced from a ponderosa pine forest and an agricultural field, we performed a greenhouse experiment that used a crossed design to test the individual and combined effects of the water availability and the soil microbiome composition on plant performance. Specifically, we studied the structural and leaf functional traits of maize that are relevant to drought tolerance. We further examined how microbial relationships with plant phenotypes varied under different combinations of microbial composition and water availability. We found that water availability and microbial composition affected plant structural traits. Surprisingly, they did not alter leaf function. Maize grown in the forest-soil microbiome produced larger plants under well-watered and water-limited conditions, compared to an agricultural soil community. Although leaf functional traits were not significantly different between the watering and microbiome treatments, the bacterial composition and abundance explained significant variability in both plant structure and leaf function within individual treatments, especially water-limited plants. Our results suggest that bacteria-plant interactions that promote plant performance under stress depend upon the greater community composition and the abiotic environment. IMPORTANCE Globally, drought is an increasingly common and severe stress that causes significant damage to agricultural and wild plants, thereby threatening food security. Despite growing evidence of the potential benefits of soil microorganisms on plant performance under stress, decoupling the effects of the microbiome composition versus the water availability on plant growth and performance remains a challenge. We used a highly controlled and replicated greenhouse experiment to understand the impacts of microbial community composition and water limitation on corn growth and drought-relevant functions. We found that both factors affected corn growth, and, interestingly, that individual microbial relationships with corn growth and leaf function were unique to specific watering/microbiome treatment combinations. This finding may help explain the inconsistent success of previously identified microbial inocula in improving plant performance in the face of drought, outside controlled environments.

Integrating nanotechnology with plant microbiome for next-generation crop health

Nanotechnology has enormous potential for sustainable agriculture, such as improving nutrient use efficiency, plant health, and food production. Nanoscale modulation of the plant-associated microbiota offers an additional valuable opportunity to increase global crop production and ensure future food and nutrient security. Nanomaterials (NMs) applied to agricultural crops can impact plant and soil microbiota, which offers valuable services to host plants, including the acquisition of nutrients, abiotic stress tolerance, and disease suppression. Dissecting the complex interactions between NMs and plants by integrating multi-omic approaches is providing new insights into how NMs can activate host responses and functionality as well as influence native microbial communities. Such nexus and moving beyond descriptive microbiome studies to hypothesis-driven research will foster microbiome engineering and open up opportunities for the development of synthetic microbial communities to provide agronomic solutions. Herein, we first summarize the significant role of NMs and the plant microbiome in crop productivity and then focus on NMs effects on plant-associated microbiota. We outline three urgent priority research areas and call for a transdisciplinary collaborative approach, involving plant scientists, soil scientists, environmental scientists, ecologists, microbiologists, taxonomists, chemists, physicists, and stakeholders, to advance nano-microbiome research. Detailed understanding of the nanomaterial-plant-microbiome interactions and the mechanisms underlying NMs-mediated shifts in the microbiome assembly and functions may help to exploit the services of both nano-objects and microbiota for next-generation crop health.

Harnessing Native Bacillus spp. for Sustainable Wheat Production

The genus Bacillus has been widely applied in contemporary agriculture as an environmentally-friendly biological agent. However, the real effect of commercial Bacillus-based fertilizers and pesticides varies immensely in the field. To harness Bacillus for efficient wheat production, we reviewed the diversity, functionality, and applicability of wheat-associated native Bacillus for the first time. Our main findings are: (i) Bacillus spp. inhabit the rhizosphere, root, stem, leaf, and kernel of wheat; (ii) B. subtilis and B. velezensis are the most widely endophytic species that can be isolated from both below and aboveground tissues; (iii) major functions of these representative strains are promotion of plant growth and alleviation of both abiotic and biotic stresses in wheat; (iv) stability and effectiveness are 2 major challenges during field application; (v) a STVAE pipeline that includes 5 processes, namely, Screen, Test, Validation, Application, and Evaluation, has been proposed for the capture and refinement of wheat-associated Bacillus spp. In particular, this review comprehensively addresses possible solutions, concerns, and criteria during the development of native Bacillus-based inoculants for sustainable wheat production.

PGPR: the treasure of multifarious beneficial microorganisms for nutrient mobilization, pest biocontrol and plant growth promotion in field crops

Plant growth-promoting rhizobacteria (PGPR) have multifarious beneficial activities for plant growth promotion; act as source of metabolites, enzymes, nutrient mobilization, biological control of pests, induction of disease resistance vis-a-vis bioremediation potentials by phytoextraction and detoxification of heavy metals, pollutants and pesticides. Agrochemicals and synthetic pesticides are currently being utilized widely in all major field crops, thereby adversely affecting human and animal health, and posing serious threats to the environments. Beneficial microorganisms like PGPR could potentially substitute and supplement the toxic chemicals and pesticides with promising application in organic farming leading to sustainable agriculture practices and bioremediation of heavy metal contaminated sites. Among field crops limited bio-formulations have been prepared till now by utilization of PGPR strains having plant growth promotion, metabolites, enzymes, nutrient mobilization and biocontrol activities. The present review contributes comprehensive description of PGPR applications in field crops including commercial, oilseeds, leguminous and cereal crops to further extend the utilization of these potent groups of beneficial microorganisms so that even higher level of crop productivity and quality produce of field crops could be achieved. PGPR and bacteria based commercialized bio-formulations available worldwide for its application in the field crops have been compiled in this review which can be a substitute for the harmful synthetic chemicals. The current knowledge gap and potential target areas for future research have also been projected.

Co-inoculation of antagonistic Bacillus velezensis FH-1 and Brevundimonas diminuta NYM3 promotes rice growth by regulating the structure and nitrification function of rhizosphere microbiome

Microbial inoculation with plant growth-promoting microorganisms (PGPMs) is one of the most promising technologies to solve the current global challenges. Co-inoculants is more efficient and stable than mono-inoculants. However, the growth promoting mechanism of co-inoculants in complex soil system is still poorly understood. In this study, the effects on rice, soil and the microbiome of the mono-inoculant Bacillus velezensis FH-1 (F) and Brevundimonas diminuta NYM3 (N) and the co-inoculant FN obtained in previous works were compared. Correlation analysis and PLS-PM were used to explore the primary mechanism of different inoculants promoting rice growth. We hypothesized that inoculants promoted plant growth (i) by themselves, (ii) by improving soil nutrient availability or (iii) by regulating the rhizosphere microbiome in complex soil system. We also assumed that different inoculants had different ways of promoting plant growth. The results showed that FN significantly promoted rice growth and nitrogen absorption and slightly increased soil total nitrogen and microbial network complexity compared with F, N and the control (CK). B. velezensis FH-1 and B. diminuta NYM3 interfered with each other's colonization in FN. FN increased the complexity of the microbial network compared to F and N. The bacterial community of FN was quite different from CK and N, while the fungal community was not significantly different from other treatments. The species and functions enriched or inhibited by FN are part of F. The correlation analysis and PLS-PM results showed that inoculants (F/N/FN) promoted the growth of rice mainly by regulating the rhizosphere microbiome rather than by themselves or by improving soil nutrient availability. Co-inoculant FN promotes rice growth specifically by enhancing microbial nitrification function through enriching related species compared with F or N. This may provide theoretical guidance for the construction and application of co-inoculants in the future.

Leveraging microbiome rediversification for the ecological rescue of soil function

BACKGROUND

Global biodiversity losses threaten ecosystem services and can impact important functional insurance in a changing world. Microbial diversity and function can become depleted in agricultural systems and attempts to rediversify agricultural soils rely on either targeted microbial introductions or retaining natural lands as biodiversity reservoirs. As many soil functions are provided by a combination of microbial taxa, rather than outsized impacts by single taxa, such functions may benefit more from diverse microbiome additions than additions of individual commercial strains. In this study, we measured the impact of soil microbial diversity loss and rediversification (i.e. rescue) on nitrification by quantifying ammonium and nitrate pools. We manipulated microbial assemblages in two distinct soil types, an agricultural and a forest soil, with a dilution-to-extinction approach and performed a microbiome rediversification experiment by re-introducing microorganisms lost from the dilution. A microbiome water control was included to act as a reference point. We assessed disruption and potential restoration of (1) nitrification, (2) bacterial and fungal composition through 16S rRNA gene and fungal ITS amplicon sequencing and (3) functional genes through shotgun metagenomic sequencing on a subset of samples.

RESULTS

Disruption of nitrification corresponded with diversity loss, but nitrification was successfully rescued in the rediversification experiment when high diversity inocula were introduced. Bacterial composition clustered into groups based on high and low diversity inocula. Metagenomic data showed that genes responsible for the conversion of nitrite to nitrate and taxa associated with nitrogen metabolism were absent in the low diversity inocula microcosms but were rescued with high diversity introductions.

CONCLUSIONS

In contrast to some previous work, our data suggest that soil functions can be rescued by diverse microbiome additions, but that the concentration of the microbial inoculum is important. By understanding how microbial rediversification impacts soil microbiome performance, we can further our toolkit for microbial management in human-controlled systems in order to restore depleted microbial functions.

Liquid biofertilizers as a sustainable solution for agriculture

This paper provides a mini review of liquid biofertilizers, which have been proven to perform better than the other forms in lasting for longer periods of time, improving crop quality, and requiring less amounts for application. The production of liquid biofertilizers, types of liquid inoculants, and their effect on plant growth are covered in this review. Liquid biofertilizers can be made from wastes and by-products of several industries, making zero or near-zero discharge possible and thus gearing towards circular economy. Despite their usefulness in enhancing crop quality and eco-friendliness, in order to compete with chemical fertilizers, there are a number of challenges to overcome, such as extending the shelf life, making them more susceptible to seasonal climate conditions and soil types, and development of suitable machineries for production and application. More field trials, cost-benefit analysis and long-term studies should also be evaluated for commercialization purposes.