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Saline soils pose significant challenges to global agricultural productivity, hindering crop growth and efficiency. Despite various mitigation strategies, the issue persists, underscoring the need for innovative and sustainable solutions. One promising approach involves leveraging microorganisms and their plant interactions to reclaim saline soils and bolster crop yields. This review highlights pioneering and recent advancements in utilizing multi-traits Trichoderma and Bacillus species as potent promoters of plant growth and health. It examines the multifaceted impacts of saline stress on plants and microbes, elucidating their physiological and molecular responses. Additionally, it delves into the role of ACC deaminase in mitigating plant ethylene levels by Trichoderma and Bacillus species. Although there are several studies on Trichoderma-Bacillus, much remains to be understood about their synergistic relationships and their potential as auxiliaries in the phytoremediation of saline soils, which is why this work addresses these challenges.

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There is an increasing demand for bioinoculants based on plant growth-promoting rhizobacteria (PGPR) for use in agricultural ecosystems. However, there are still concerns and limited data on their reproducibility in different soil types and their effects on endemic rhizosphere communities. Therefore, this study explored the effects of inoculating the PGPR, Pseudomonas fluorescens strain UM270, on maize growth (Zea mays L.) and its associated rhizosphere bacteriome by sequencing the 16S ribosomal genes under greenhouse conditions. The results showed that inoculation with PGPR P. fluorescens UM270 improved shoot and root dry weights, chlorophyll concentration, and total biomass in the three soil types evaluated (clay, sandy-loam, and loam) compared to those of the controls. Bacterial community analysis of the three soil types revealed that maize plants inoculated with the UM270 strain showed a significant increase in Proteobacteria and Acidobacteria populations, whereas Actinobacteria and Bacteroidetes decreased. Shannon, Pielou, and Faith alpha-biodiversity indices did not reveal significant differences between treatments. Beta diversity revealed a bacterial community differential structure in each soil type, with some variation among treatments. Finally, some bacterial groups were found to co-occur and co-exclude with respect to UM270 inoculation. Considered together, these results show that PGPR P. fluorescens UM270 increases maize plant growth and has an important effect on the resident rhizobacterial communities of each soil type, making it a potential agricultural biofertilizer.

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Soil salinity is one of the most important abiotic factors that affects agricultural production worldwide. Because of saline stress, plants face physiological changes that have negative impacts on the various stages of their development, so the employment of plant growth-promoting bacteria (PGPB) is one effective means to reduce such toxic effects. Bacteria of the Bacillus genus are excellent PGPB and have been extensively studied, but what traits makes them so extraordinary to adapt and survive under harsh situations? In this work we review the Bacillus' innate abilities to survive in saline stressful soils, such as the production osmoprotectant compounds, antioxidant enzymes, exopolysaccharides, and the modification of their membrane lipids. Other survival abilities are also discussed, such as sporulation or a reduced growth state under the scope of a functional interaction in the rhizosphere. Thus, the most recent evidence shows that these saline adaptive activities are important in plant-associated bacteria to potentially protect, direct and indirect plant growth-stimulating activities. Additionally, recent advances on the mechanisms used by Bacillus spp. to improve the growth of plants under saline stress are addressed, including genomic and transcriptomic explorations. Finally, characterization and selection of Bacillus strains with efficient survival strategies are key factors in ameliorating saline problems in agricultural production.

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The growing human population has a greater demand for food; however, the care and preservation of nature as well as its resources must be considered when fulfilling this demand. An alternative employed in recent decades is the use and application of microbial inoculants, either individually or in consortium. The transplantation of rhizospheric microbiomes (rhizobiome) recently emerged as an additional proposal to protect crops from pathogens. In this review, rhizobiome transplantation was analyzed as an ecological alternative for increasing plant protection and crop production. The differences between single-strain/species inoculation and dual or consortium application were compared. Furthermore, the feasibility of the transplantation of other associated micro-communities, including phyllosphere and endosphere microbiomes, were evaluated. The current and future challenges surrounding rhizobiome transplantation were additionally discussed. In conclusion, rhizobiome transplantation emerges as an attractive alternative that goes beyond single/group inoculation of microbial agents; however, there is still a long way ahead before it can be applied in large-scale agriculture.

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Biocontrol agents (BCA) have been an important tool in agriculture to prevent crop losses due to plant pathogens infections and to increase plant food production globally, diminishing the necessity for chemical pesticides and fertilizers and offering a more sustainable and environmentally friendly option. Fungi from the genus Trichoderma are among the most used and studied microorganisms as BCA due to the variety of biocontrol traits, such as parasitism, antibiosis, secondary metabolites (SM) production, and plant defense system induction. Several Trichoderma species are well-known mycoparasites. However, some of those species can antagonize other organisms such as nematodes and plant pests, making this fungus a very versatile BCA. Trichoderma has been used in agriculture as part of innovative bioformulations, either just Trichoderma species or in combination with other plant-beneficial microbes, such as plant growth-promoting bacteria (PGPB). Here, we review the most recent literature regarding the biocontrol studies about six of the most used Trichoderma species, T. atroviride, T. harzianum, T. asperellum, T. virens, T. longibrachiatum, and T. viride, highlighting their biocontrol traits and the use of these fungal genera in Trichoderma-based formulations to control or prevent plant diseases, and their importance as a substitute for chemical pesticides and fertilizers.

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Phytohormones are regulators of plant growth and development, which under different types of stress can play a fundamental role in a plant's adaptation and survival. Some of these phytohormones such as cytokinin, gibberellin, salicylic acid, auxin, and ethylene are also produced by plant growth-promoting bacteria (PGPB). In addition, numerous volatile organic compounds are released by PGPB and, like bacterial phytohormones, modulate plant physiology and genetics. In the present work we review the basic functions of these bacterial phytohormones during their interaction with different plant species. Moreover, we discuss the most recent advances of the beneficial effects on plant growth of the phytohormones produced by PGPB. Finally, we review some aspects of the cross-link between phytohormone production and other plant growth promotion (PGP) mechanisms. This work highlights the most recent advances in the essential functions performed by bacterial phytohormones and their potential application in agricultural production.

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Botrytis cinerea is the causal agent of grey mould and one of the most important plant pathogens in the world because of the damage it causes to fruits and vegetables. Although the application of botrycides is one of the most common plant protection strategies used in the world, the application of plant-beneficial bacteria might replace botrycides facilitating agroecological production practices. Based on this, we reviewed the different stages of B. cinerea infection in plants and the biocontrol mechanisms exerted by plant-beneficial bacteria, including the well-known plant growth-promoting bacteria (PGPB). Some PGPB mechanisms to control grey mould disease include antibiosis, space occupation, nutrient uptake, ethylene modulation, and the induction of plant defence mechanisms. In addition, recent studies on the action of anti-Botrytis compounds produced by PGPB and how they damage the conidial and mycelial structures of the pathogen are reviewed. Likewise, the advantages of individual inoculations of PGPB versus those that require the joint action of antagonist agents (microbial consortia) are discussed. Finally, it should be emphasised that PGPB are an excellent option to prevent grey mould in different crops and their use should be expanded for environmentally friendly agricultural practices.

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Drought intensity that has increased as a result of human activity and global warming poses a serious danger to agricultural output. The demand for ecologically friendly solutions to ensure the security of the world's food supply has increased as a result. Plant growth-promoting rhizobacteria (PGPR) treatment may be advantageous in this situation. PGPR guarantees the survival of the plant during a drought through a variety of processes including osmotic adjustments, improved phytohormone synthesis, and antioxidant activity, among others and these mechanisms also promote the plant's development. In addition, new developments in omics technology have improved our understanding of PGPR, which makes it easier to investigate the genes involved in colonizing plant tissue. Therefore, this review addresses the mechanisms of PGPR in drought stress resistance to summarize the most current omics-based and molecular methodologies for exploring the function of drought-responsive genes. The study discusses a detailed mechanistic approach, PGPR-based bioinoculant design, and a potential roadmap for enhancing their efficacy in combating drought stress.

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Bacillus sp. strain FSQ1 was isolated from the common bean (Phaseolus vulgaris L.). The genome of this strain presented 3,598,499 bp; 43.0% G + C content; 925,913 bp N50; 2 L50; 33 contigs; 97 RNAs and 3,908 predicted coding DNA sequences (CDS) distributed in 315 subsystems. Based on genome mining, the biological control activity of strains FSQ1 could be associated with the biosynthesis of rhizocticin A and bacillibactin. Thus, this strain is a promising active ingredient for the formulation of biopesticides.

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The geothermal zone of Araró, México, is located within the trans-Mexican volcanic belt, an area with numerous arsenic (As)-rich hot springs. In this study, the draft genome sequence of two endemic Bacillus strains (ZAP17 and ZAP62) from Araró microbial mat hot springs was determined, which were able to grow on arsenate As(V) (up to 64 mM) and arsenite As(III) (up to 32 mM). Phylogenetic analysis based on 16 S rRNA and gyrB sequences, as well as genome sequence analysis based on average nucleotide identity (>96 %) and digital DNA-DNA hybridization (>70 %), indicated that these strains belong to the Bacillus paralicheniformis ZAP17 and Bacillus altitudinis ZAP62. Furthermore, through genome mining, it was identified two arsenic resistance operons, arsRBC, and arsRBCDA in both strains as potential determinants of As resistance. Predicted ArsA (arsenial pump-driving ATPase), ArsB (Arsenical efflux pump protein), ArsC (Arsenate reductase), ArsD (Arsenical efflux pump protein) and ArsR (Metalloregulator/ars operon repressor) proteins, clearly grouped with their respective clades corresponding to other characterized bacterial species, mainly Firmicutes. To further evaluate the functionality of the ars operons in ZAP17 and ZAP62 strains, our results showed that arsRBC and arsRBCDA genes were expressed in the presence of As(III). Finally, the presence of ars operons in the genome of Bacillus species residing in As-rich environments, such as the Araró hot springs, might be a potential mechanism to survive under such harsh conditions.

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Crop plants are affected by a series of inhibitory environmental and biotic factors that decrease their growth and production. To counteract these adverse effects, plants work together with the microorganisms that inhabit their rhizosphere, which is part of the soil influenced by root exudates. The rhizosphere is a microecosystem where a series of complex interactions takes place between the resident microorganisms (rhizobiome) and plant roots. Therefore, this study analyzes the dynamics of plant-rhizobiome communication, the role of exudates (diffusible and volatile) as a factor in stimulating a diverse rhizobiome, and the differences between rhizobiomes of domesticated crops and wild plants. The study also analyzes different strategies to decipher the rhizobiome through both classical cultivation techniques and the so-called "omics" sciences. In addition, the rhizosphere engineering concept and the two general strategies to manipulate the rhizobiome, i.e., top down and bottom up engineering have been revisited. In addition, recent studies on the effects on the indigenous rhizobiome of inoculating plants with foreign strains, the impact on the endobiome, and the collateral effects on plant crops are discussed. Finally, understanding of the complex rhizosphere interactions and the biological repercussions of rhizobiome engineering as essential steps for improving plant growth and health is proposed, including under adverse conditions.

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Plants and their microbiomes, including plant growth-promoting bacteria (PGPB), can work as a team to reduce the adverse effects of different types of stress, including drought, heat, cold, and heavy metals stresses, as well as salinity in soils. These abiotic stresses are reviewed here, with an emphasis on salinity and its negative consequences on crops, due to their wide presence in cultivable soils around the world. Likewise, the factors that stimulate the salinity of soils and their impact on microbial diversity and plant physiology were also analyzed. In addition, the saline soils that exist in Mexico were analyzed as a case study. We also made some proposals for a more extensive use of bacterial bioinoculants in agriculture, particularly in developing countries. Finally, PGPB are highly relevant and extremely helpful in counteracting the toxic effects of soil salinity and improving crop growth and production; therefore, their use should be intensively promoted.

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The endophytic bacterial diversity of root, stem, and leaf tissues of Mexican husk tomato plants (Physalis ixocarpa) was compared and deciphered, and screened for their plant growth-promoting activity and antagonism against fungal phytopathogens. Total 315 isolates (108 roots, 102 stems, and 105 leaves) were obtained and characterized by 16S ribosomal gene sequencing. The most abundant genera were Bacillus, Microbacterium, Pseudomonas, and Stenotrophomonas. Unique species were found for each tissue analyzed, along with B. thuringiensis, B. toyonensis, Neobacillus drentensis, Paenibacillus castaneae, P. fluorescens, P. poae, and S. maltophilia present throughout the plant. Biodiversity indices did not show significant differences, but root tissues showed the highest abundance of bacterial endophytes. Several isolates showed excellent promotion activities in Physalis ixocarpa seedlings, increasing the length and weight of the root, total biomass, and chlorophyll content. Various isolates also exhibited antagonism against fungal pathogens. Among screened isolates, Neobacillus drentensis CH23 was found in all plant compartments, exhibiting growth-promoting activity and fungal antagonism. Strain CH23 and other endophytes showed the production of indoleacetic acid, siderophores, proteases, and solubilization of phosphates. These results demonstrate that the husk tomato plant endobiome has a high potential as a bioinoculating agent for agriculturally important crops.

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The application of plant growth-promoting rhizobacteria (PGPR) in the field has been hampered by a number of gaps in the knowledge of the mechanisms that improve plant growth, health, and production. These gaps include (i) the ability of PGPR to colonize the rhizosphere of plants and (ii) the ability of bacterial strains to thrive under different environmental conditions. In this review, different strategies of PGPR to colonize the rhizosphere of host plants are summarized and the advantages of having highly competitive strains are discussed. Some mechanisms exhibited by PGPR to colonize the rhizosphere include recognition of chemical signals and nutrients from root exudates, antioxidant activities, biofilm production, bacterial motility, as well as efficient evasion and suppression of the plant immune system. Moreover, many PGPR contain secretion systems and produce antimicrobial compounds, such as antibiotics, volatile organic compounds, and lytic enzymes that enable them to restrict the growth of potentially phytopathogenic microorganisms. Finally, the ability of PGPR to compete and successfully colonize the rhizosphere should be considered in the development and application of bioinoculants.

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Sustainable agriculture requires the recruitment of bacterial agents to control diverse plant diseases such as bacterial endophytes. Bacterial endophytes colonize and inhabit internal plant tissues without causing any apparent damage. Within the plant, these bacteria exert multiple beneficiary effects, including direct stimulation of plant growth by the action of phytohormones or the production of metabolites. However, bacterial endophytes also protect their plant host through biocontrol pathogens or by inducing plant innate immune system. The present work makes a systematic and in-depth review on the current state of endophytic bacterial diversity, their plant colonization strategies, and their potential roles as protective agents against plant diseases during pre- and post-harvest stages of crop productivity. In addition, an exploration of their beneficial effects on sustainable agriculture by reducing/eliminating the use of toxic agrochemicals was conducted. Finally, we propose diverse effective strategies for the application of endophytic bacteria as biological agents during both pre- and post-harvest stages, with the aim of protecting crop plants and their agricultural products.

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Here we report the draft genome sequence of bacterial strain CR71, consisting of a single chromosome with 5,914,775 base pairs (bp), 34.7% G + C content, and 5733 protein-coding genes. Phylogenetic analysis indicates that the CR71 strain is affiliated with Bacillus thuringiensis species, with an average nucleotide identity > 96% and genome to genome distance > 70%. The genome of B. thuringiensis strain CR71 contains genes potentially involved in a wide variety of both plant pathogen-antagonistic and plant-growth-promoting activities, such as biofilm production; acetoin, butanediol, and indoleacetic acid (IAA) synthesis; production of quorum-sensing molecules; synthesis of toxins and lytic enzymes; and promotion of tolerance to oxidative, metal, and salt stress. Additionally, antiSMASH analysis revealed a potential synthesis of siderophores and peptide antibiotics. To confirm the in silico data, strain CR71 was inoculated into cucumber plants (Cucumis sativus L.) in a field trial, in which we observed an increase in stem thickness, as well as shoot fresh weight and length. Importantly, compared to un-inoculated control plants, plants inoculated with strain CR71 increased the size/weight ratio of cucumber fruits (34.99%), biovolume index (16.8%), and total fruit yield (34.97%). In conclusion, genome analysis of strain CR71 confirmed multifactorial plant-beneficial mechanisms and the potential of CR71 as an agricultural bio-inoculant.

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Salinity in agricultural soil is a major problem around the world, with negative consequences for the growth and production of a wide range of crops. To counteract these harmful effects, plants sometimes have bacterial partners that contain the enzyme 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, which acts by degrading ACC (the precursor of ethylene in all higher plants). The enzymatic activity of ACC deaminase results in the production of α-ketobutyrate and ammonia, which, by lowering ACC levels, prevents excessive increases in the synthesis of ethylene under various stress conditions and is one of the most efficient mechanisms to induce plant tolerance to salt stress. In the present review, recent works on the role of ACC deaminase are discussed alongside its importance in promoting plant growth under conditions of salt stress in endophytic and rhizospheric bacteria, with some emphasis on Bacillus species. In addition, the toxic effects of soil salinity on plants and microbial biodiversity are analysed. Recent findings on the synergetic functioning of ACC deaminase and other bacterial mechanisms of salt stress tolerance, such as trehalose accumulation, are also summarized. Finally, we discuss the various advantages of ACC deaminase-producing bacilli as bioinoculants to address the problem of salinity in agricultural soils.

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In this work, we report an analysis of the draft genome of the blueberry (Vaccinium spp. var. Biloxi) growth-promoting endophyte Bacillus toyonensis, strain COPE52. The genome of COPE52 consists of a single 5,806,513 bp replicon, with a 35.1% G + C content. Strain COPE52 was strongly affiliated to B. toyonensis species, based on species delimitation cut-off values established for average nucleotide identity (> 95-96%), genome-to genome distance calculator (> 70%) and phylogenomic analysis. The RAST genomic annotation of the COPE52 strain revealed a total of 5979 total genes, including 5631 protein-coding genes, 11 rRNA genes, 5 ncRNAs, 81 tRNA genes, and 251 pseudogenes. To further validate the in silico analysis results, experiments were carried out to detect the production of indoleacetic acid, protease activity, and the emission of volatiles like acetoin, 2,3-butanediol and dimethyl disulphide as potential plant growth-promoting mechanisms. COPE52 also showed antifungal action against the grey mould phytopathogen, Botrytis cinerea, during in vitro bioassays. In addition, inoculation with strain COPE52 promoted growth biomass and chlorophyll content in blueberry plants (Vaccinium spp. var. Biloxi) under greenhouse conditions. To our knowledge, this is the first study showing genomic and experimental evidence of B. toyonensis as plant growth-promoting bacteria (PGPB).

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Soil salinity is a major problem in agriculture. However, crop growth and productivity can be improved by the inoculation of plants with beneficial bacteria that promote plant growth under stress conditions such as high salinity. Here, we evaluated 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity and trehalose accumulation of the plant growth promoting bacterium Pseudomonas sp. UW4. Mutant strains (mutated at acdS, treS, or both) and a trehalose over-expressing strain (OxtreS) were constructed. The acdS mutant was ACC deaminase minus; the treS- strain significantly decreased its accumulation of trehalose, and the double mutant was affected in both characteristics. The OxtreS strain accumulated more trehalose than the wild-type strain UW4. Inoculating tomato plants subjected to salt stress with these strains significantly impacted root and shoot length, total dry weight, and chlorophyll content. The evaluated parameters in the single acdS and treS mutants were impaired. The double acdS/treS mutant was negatively affected to a greater extent than the single-gene mutants, suggesting a synergistic action of these activities in the protection of plants against salt stress. Finally, the OxtreS overproducing strain protected tomato plants to a greater extent under stress conditions than the wild-type strain. Taken together, these results are consistent with the synergistic action of ACC deaminase and trehalose in Pseudomonas sp. UW4 in the protection of tomato plants against salt stress.

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A plant microbiome includes a microbial community that typically interacts extensively with a plant. The plant microbiome can survive either inside or outside of plant tissues, performing various plant beneficial activities including biocontrol of potential phytopathogens and promotion of plant growth. An important part of the plant microbiome includes plant growth-promoting bacteria (PGPB) that commonly reside in the rhizosphere and phyllosphere, and as endophytic bacteria (inside of plant tissues). As new plant microbiome-manipulating strategies have emerged in recent years, we have critically reviewed relevant literature, chiefly from the last decade. We have analysed and compared the rhizosphere, phyllosphere and endosphere as potential ecosystems for manipulation, in order to improve positive interactions with the plant. In addition, many studies on the bioengineering of the endophyte microbiome and its potential impact on the core microbiome were analysed with respect to five different strategies, including host mediated and multi-generation microbiome selection, inoculation into soil and rhizosphere, inoculations into seeds or seedlings, tissue atomisation and direct injection into tissues or wounds. Finally, microbiome engineering presents a feasible strategy to solve multiple agriculture-associated problems in an eco-friendly way.

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