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The use of plant growth-promoting bacteria as bioinoculants is a powerful tool to increase crop yield and quality and to improve nitrogen use efficiency (NUE) from fertilizers in plants. This study aimed to bioprospecting a native bacterial consortium (Bacillus cabrialesii subsp. cabrialesii TE3T, Priestia megaterium TRQ8, and Bacillus paralicheniformis TRQ65), through bioinformatic analysis, and to quantify the impact of its inoculation on NUE (measured through 15N-isotopic techniques), grain yield, and grain quality of durum wheat variety CIRNO C2008 grown under three doses of urea (0, 120, and 240 kg N ha-1) during two consecutive agricultural cycles in the Yaqui Valley, Mexico. The inoculation of the bacterial consortium (BC) to the wheat crop, at a total N concentration of 123-225 kg N ha-1 increased crop productivity and maintained grain quality, resulting in a yield increase of 1.1 ton ha-1 (6.0 vs. 7.1 ton ha-1, 0 kg N ha-1 added, 123 kg N ha-1 in the soil) and of 2.0 ton ha-1 (5.9 vs. 7.9 ton ha-1, 120 kg N ha-1 added, 104 kg N ha-1 in the soil) compared to the uninoculated controls at the same doses of N. The genomic bioinformatic analysis of the studied strains showed a great number of biofertilization-related genes regarding N and Fe acquisition, P assimilation, CO2 fixation, Fe, P, and K solubilization, with important roles in agroecosystems, as well as genes related to the production of siderophores and stress response. A positive effect of the BC on NUE at the studied initial N content (123 and 104 kg N ha-1) was not observed. Nevertheless, increases of 14 % and 12.5 % on NUE (whole plant) were observed when 120 kg N ha-1 was applied compared to when wheat was fully fertilized (240 kg N ha-1). This work represents a link between bioinformatic approaches of a native bacterial inoculant and the quantification of its impact on durum wheat.
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Strain CMT1 was isolated from nodules of non-inoculated Roundup Ready (RR) soybean plants (Glycine max L. Merrill), which were collected in fields in Itauguá, Paraguay. The genome of this strain had 338,984,909 bp; 59.2 % G + C content; 377648 bp N50; 5 L50; 55 contigs; 51 RNAs and 5,272 predicted coding DNA sequences (CDS) distributed in 327 subsystems. Based on overall genome-relatedness indices (OGRIs), this strain was taxonomically affiliated with Agrobacterium pusense. Based on genome mining, strain CMT1 is a promising plant growth-promoting bacterium that could be validated in agricultural fields for increasing soybean yield and quality, diminishing the economic, environmental, and health costs of non-sustainable food production.
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Fungal plant pathogens are responsible for serious losses in many economically important crop species worldwide. Due to the use of fungicides and the fungi genome plasticity, multi-drug resistant strains are emerging as a new generation of pathogens, causing an expansive range of superficial and systemic plant infections, or new opportunistic fungal pathogens for humans. The group of antagonistic fungi Trichoderma spp. has been widely used to enhance plant growth and for the control of different pathogens affecting crops. Although Neurospora crassa is not a mycoparasitic fungus, its secretion of secondary metabolites with antimicrobial activity has been described. In this work, the effect of crude extract of the monoculture of Trichoderma asperellum T8a or the co-culture with N. crassa as an inhibitory treatment against the fungal pathogens Botrytis cinerea and Fusarium solani was evaluated. The findings demonstrate that the secondary metabolites contained in the T. asperellum crude extract have a clear fungistatic activity against B. cinerea and F. solani. Interestingly, this fungistatic activity highly increases when T. asperellum is co-cultivated with the non-pathogenic fungus N. crassa. Moreover, the co-culture crude extract also showed antifungal activity on post-harvest fruits, and no toxic effects on Murine fibroblast L929 (CCL-1) and murine macrophages RAW 264.7 (TIB-71) were observed. All these results together are solid evidence of the potential of the co-culture crude extract of T. asperellum and N. crassa, as an antifungal agent against phytopathogenic fungi, or post-harvest fruits during the transportation or commercialization time.
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Botrytis , Técnicas de Cocultura , Frutas , Fusarium , Trichoderma , Fusarium/efeitos dos fármacos , Fusarium/crescimento & desenvolvimento , Frutas/microbiologia , Frutas/química , Botrytis/efeitos dos fármacos , Botrytis/crescimento & desenvolvimento , Trichoderma/metabolismo , Trichoderma/genética , Animais , Camundongos , Antifúngicos/farmacologia , Antifúngicos/metabolismo , Doenças das Plantas/microbiologia , Doenças das Plantas/prevenção & controle , Neurospora crassa/efeitos dos fármacos , Neurospora crassa/metabolismo , Células RAW 264.7 , Misturas Complexas/farmacologia , Misturas Complexas/químicaRESUMO
The use of plant-associated microorganisms is increasingly being investigated as a key tool for mitigating the impact of biotic and abiotic threats to crops and facilitating migration to sustainable agricultural practices. The microbiome is responsible for several functions in agroecosystems, such as the transformation of organic matter, nutrient cycling, and plant/pathogen growth regulation. As climate change and global warming are altering the dynamics of plant-microbial interactions in the ecosystem, it has become essential to perform comprehensive studies to decipher current and future microbial interactions, as their useful symbiotic mechanisms could be better exploited to achieve sustainable agriculture. This will allow for the development of effective microbial inoculants that facilitate nutrient supply for the plant at its minimal energy expense, thus increasing its resilience to biotic and abiotic stresses. This article collection aims to compile state-of-the-art research focused on the elucidation and optimization of symbiotic relationships between crops and their associated microbes. The information presented here will contribute to the development of next-generation microbial inoculants for achieving a more sustainable agriculture.
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Microbiota , Simbiose , Produtos Agrícolas , Agricultura , Mudança ClimáticaRESUMO
Maize (Zea mays) is an influential crop in its production across the world. However, the invasion of many phytopathogens greatly affects the maize crop yield at various hotspot areas. Of many diseases, bacterial stalk rot of maize caused by Dickeya zeae results in severe yield reduction, thus the need for efficient management is important. Further, to produce epidemiological information for control of disease outbreaks in the hot spot regions of Sialkot District, Punjab Pakistan, extensive field surveys during 2021 showed that out of 266 visited areas, the highest disease incidence ranging from 66.5 to 78.5% while the lowest incidence was ranging from 9 to 20%. The Maxent modeling revealed that among 19 environmental variables, four variables including temperature seasonality (bio-4), mean temperature of the wettest quarter (bio-8), annual precipitation (bio-12), and precipitation of driest month (bio-14) were significantly contributing to disease distribution in current and coming years. The study outcomes revealed that disease spread will likely increase across four tehsils of Sialkot over the years 2050 and 2070. Our findings will be helpful to policymakers and researchers in devising effective disease management strategies against bacterial stalk rot of maize outbreaks in Sialkot, Pakistan.
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Mudança Climática , Dickeya , Zea mays , Zea mays/microbiologia , Paquistão , Doenças das Plantas/microbiologia , EnterobacteriaceaeRESUMO
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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Bacillus , Bacillus/fisiologia , Solo , Raízes de Plantas/microbiologia , Bactérias/genética , AntioxidantesRESUMO
The preparation method of hydrogels has a significant effect on their structural and physicochemical properties. In this report, physically and chemically cross-linked poly(vinyl alcohol) (PVA) networks containing humic acid (HA) were alternatively prepared by autoclaving (AC) and through glutaraldehyde (GA) addition, respectively, for agricultural purposes. PVA/HA hydrogels were comparatively characterized by Fourier transform infrared spectroscopy, thermogravimetric analysis, mechanical assays, scanning electron microscopy, swelling kinetics measurements, and water retention tests in soil. AC hydrogels showed a more homogeneous porous microstructure, higher swelling levels, and a better capacity to preserve the humidity of soil than those obtained by adding GA. Both PVA/HA hydrogels exhibited no phytotoxicity on cultivation trials of Sorghum sp., but the plant growth was promoted with the GA-cross-linked network as compared to the effect of the AC sample. The release behavior of urea was modified according to the preparation method of the PVA/HA hydrogels. After 3 days of sustained urea release, 91% of the fertilizer was delivered from the AC hydrogel, whereas a lower amount of 56% was released for the GA-cross-linked hydrogel. Beyond the advantages of applying PVA/HA hydrogels in the agricultural field, an appropriate method of preparing these materials endows them with specific properties according to the requirements of the target crop.
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Strain FSQ1T was isolated from the rhizosphere of the common bean (Phaseolus vulgaris L.) crop sampled in a commercial field located in the Gabriel Leyva Solano community, which belongs to the Guasave municipality (state of Sinaloa, Mexico). Based on its full-length 16S rRNA gene sequence, strain FSQ1T was assigned to the genus Bacillus (100â% similarity). This taxonomic affiliation was supported by its morphological and metabolic traits. Strain FSQ1T was a Gram-stain-positive bacterium with the following characteristics: rod-shaped cells, strictly aerobic, spore forming, catalase positive, reduced nitrate to nitrite, hydrolysed starch and casein, grew in the presence of lysozyme and 2â% NaCl, utilized citrate, grew at pH 6.0-8.0, produced acid from glucose, was unable to produce indoles from tryptophan, and presented biological control against Sclerotinia sclerotiorum. The whole-genome phylogenetic results showed that strain FSQ1T formed an individual clade in comparison with highly related Bacillus species. In addition, the maximum values for average nucleotide identity and from Genome-to-Genome Distance Calculator analysis were 91.57 and 44.20â%, respectively, with Bacillus spizizenii TU-B-10T. Analysis of its fatty acid content showed the ability of strain FSQ1T to produce fatty acids that are not present in closely related Bacillus species, such as C18â:â0 and C20â:â0. Thus, these results provide strong evidence that strain FSQ1T represents a novel species of the genus Bacillus, for which the name Bacillus mexicanus sp. nov. is proposed. The type strain is FSQ1T (CM-CNRG TB51T=LBPCV FSQ1T).
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Bacillus , Phaseolus , Ácidos Graxos/química , México , Filogenia , RNA Ribossômico 16S/genética , Composição de Bases , DNA Bacteriano/genética , Análise de Sequência de DNA , Técnicas de Tipagem BacterianaRESUMO
Bacillus cabrialesii is a novel bacterial species isolated from wheat (Triticum turgidum L. subsp. durum) plants in the Yaqui Valley, Mexico, by our research team. Over years of research studying this strain at the cutting-edge level, it has shown different mechanisms of action. B. cabrialesii is strongly reported as a plant-growth-promoting bacterium and a biological control agent on wheat crops. Knowing this, B. cabrialesii has been brought from lab to field as part of a bacterial consortium, not to mention that there are ongoing investigations into formulating a cost-effective bioinoculant to increase the yield and/or quality of wheat. Moreover, studies of this novel species as a biocontrol agent in other crops (pepper, tomato, cucumber, and potato) are being carried out, with preliminary results that make B. cabrialesii a promising biological control agent, inhibiting the growth of phytopathogens. However, research into this bacterium has not only been reported in our country; there are many studies around the world in which promising native Bacillus strains end up being identified as B. cabrialesii, which reaffirms the fact that this bacterial species can promote plant growth and combat phytopathogens, showing great agrobiotechnological potential.
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Bacillus cabrialesii TE3T is a strictly aerobic and Gram-stain-positive plant growth-promoting bacterium, motile and catalase-positive. In addition, strain TE3T was also recently described as a biological control agent. Here, we present the complete circularized genome of this type strain, as well as a whole genome analysis identifying genes of agricultural interest. Thus, a hybrid assembly method was performed using short-read sequencing through the Illumina MiSeq platform, and long-read sequencing through the MinION sequencing technology by Oxford Nanopore Technology (ONT). This assembly method showed a closed circular chromosome of 4,125,766 bp and 44.2% G + C content. The strain TE3T genome annotation, based on the RAST platform, presented 4,282 Coding DNA sequences (CDS) distributed in 335 subsystems, from which 4 CDS are related to the promotion of plant growth and 28 CDS to biological control. Also, Prokka (Rapid Prokaryotic Genome Annotation) predicted a total of 119 RNAs composed of 87 tRNAs, 31 rRNA, and 1 tmRNA; and the PGAP (Prokaryotic Genome Annotation Pipeline) predicted a total of 4,212 genes (3,991 CDS). Additionally, seven putative biosynthetic gene clusters were identified by antiSMASH, such as Fengycin, Bacilysin, Subtilosin A, Bacillibactin, Bacillaene, Surfactin, and Rizocticin A, which are related to antimicrobial and antifungal properties, whose gene presence was further supported by the Prokaryotic Genome Annotation Pipeline (PGAP) annotation. Thus, the complete genome of Bacillus cabrialesii TE3T showed promising bioactivities for the use of this type strain to bioformulate bacterial inoculants for sustainable 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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Bio-formulation technologies have a limited impact on agricultural productivity in developing countries, especially those based on plant growth-promoting rhizobacteria. Thus, calcium alginate microbeads were synthesized and used for the protection and delivery of three beneficial Bacillus strains for agricultural applications. The process of encapsulation had a high yield per gram for all bacteria and the microbeads protected the Bacillus strains, allowing their survival, after 12 months of storage at room temperature. Microbead analysis was carried out by observing the rate of swelling and biodegradation of the beads and the released-establishment of bacteria in the soil. These results showed that there is an increase of around 75% in bead swelling on average, which allows for larger pores, and the effective release and subsequent establishment of the bacteria in the soil. Biodegradation of microbeads in the soil was gradual: in the first week, they increased their weight (75%), which consistently results in the swelling ratio. The co-inoculation of the encapsulated strain TRQ8 with the other two encapsulated strains showed plant growth promotion. TRQ8 + TRQ65 and TRQ8 + TE3T bacteria showed increases in different biometric parameters of wheat plants, such as stem height, root length, dry weight, and chlorophyll content. Thus, here we demonstrated that the application of alginate microbeads containing the studied strains showed a positive effect on wheat plants.
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BACKGROUND: The use of plant growth-promoting microorganisms represents a sustainable way to increase agricultural yields and plant health. Thus, the identification and tracking of these microorganisms are determinants for validating their positive effects on crops. Pangenomes allow the identification of singletons that can be used to design specific primers for the detection of the studied strains. OBJECTIVE: This study aimed to establish a strategy based on the use of whole-genome sequencing and pangenomes for designing and validating primer sets for detecting Bacillus cabrialesii TE3T, Priestia megaterium TRQ8, and Bacillus paralicheniformis TRQ65, a promising beneficial bacterial consortium for wheat. METHODS AND RESULTS: The identification of singletons of TE3T, TRQ8, and TRQ65 was performed by pangenomes using the Kbase platform and subsequently analyzed using BLAST®. The identified DNA regions were used for primer design in AlleleID version 7. Primers were validated by multiplex PCR using pure template DNA from each studied strain, combinations of two or three DNA from these strains, and DNA from agricultural soil samples enriched (and not) with the bacterial consortium. Here, we report the first design of primers capable of detecting and identifying the beneficial strains TE3T, TRQ8, and TRQ65. CONCLUSIONS: The use of pangenomes allowed the distinction of unique sequences that enables the design of primers for specific identification of the studied bacterial strains. This strategy can be widely used for the design of primer sets to detect other strains of interest for combating biopiracy, and commercial protection of biological products, among other applications.
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Bactérias , Desenvolvimento Vegetal , Bactérias/genética , Triticum/genética , Triticum/microbiologia , Sequenciamento Completo do Genoma , Produtos Agrícolas/genéticaRESUMO
Strain TSO9 was isolated from a commercial field of wheat (Triticum turgidum L. subsp. durum) located in the Yaqui, Valley, Mexico. Here, the genome of this strain was sequenced, obtaining a total of 5,248,515 bp; 38.0% G + C content; 1,186,514 bp N50; and 2 L50. Based on the 16S rRNA gene sequencing, strain TSO9 was affiliated with the genus Priestia. The genome annotation of Priestia sp. TSO9 contains a total of 147 RNAs, 128 tRNAs, 1 tmRNA, and 5512 coding DNA sequences (CDS) distributed into 332 subsystems, where CDS associated with agricultural purposes were identified, such as (i) virulence, disease, and defense (57 CDS) (i.e., resistance to antibiotics and toxic compounds (34 CDS), invasion and intracellular resistance (12 CDS), and bacteriocins and ribosomally synthesized antibacterial peptides (10 CDS)), (ii) iron acquisition and metabolism (36 CDS), and (iii) secondary metabolism (4 CDS), i.e., auxin biosynthesis. In addition, subsystems related to the viability of an active ingredient for agricultural bioproducts were identified, such as (i) stress response (65 CDS). These genomic traits are correlated with the metabolic background of this strain, and its positive effects on wheat growth regulation reported in this work. Thus, further investigations of Priestia sp. TSO9 are necessary to complement findings regarding its application in agroecosystems to increase wheat yield sustainably.
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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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Arsênio , Arsenicais , Bacillus , Fontes Termais , Bacillus/genética , Bacillus/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , DNA , Óperon , FilogeniaRESUMO
Plant growth, development, and productivity are adversely affected under drought conditions. Previous findings indicated that 5-aminolevulinic acid (ALA) and 24-epibrassinolide (EBL) play an important role in the plant response to adverse environmental conditions. This study demonstrated the role of ALA and EBL on oxidative stress and photosynthetic capacity of drought-stressed 'Williams' banana grown under the Egyptian semi-arid conditions. Exogenous application of either ALA or EBL at concentrations of 15, 30, and 45 mg·L-1 significantly restored plant photosynthetic activity and increased productivity under reduced irrigation; this was equivalent to 75% of the plant's total water requirements. Both compounds significantly reduced drought-induced oxidative damages by increasing antioxidant enzyme activities (superoxide dismutase 'SOD', catalase 'CAT', and peroxidase 'POD') and preserving chloroplast structure. Lipid peroxidation, electrolyte loss and free non-radical H2O2 formation in the chloroplast were noticeably reduced compared to the control, but chlorophyll content and photosynthetic oxygen evolution were increased. Nutrient uptake, auxin and cytokinin levels were also improved with the reduced abscisic acid levels. The results indicated that ALA and EBL could reduce the accumulation of reactive oxygen species and maintain the stability of the chloroplast membrane structure under drought stress. This study suggests that the use of ALA or EBL at 30 mg·L-1 can promote the growth, productivity and fruit quality of drought-stressed banana plants.
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Halomonas sp. strain BLLS135 was isolated from hypersaline soil in Mexico. Here, we present the draft genome of this strain. Its genome has 2,861 protein-coding genes, 63 tRNAs, two 16S rRNAs, five 5S rRNAs, and a single copy of 23S rRNA, with a GC content of 63.5%.
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MAIN CONCLUSIONS: Bacillus paralicheniformis TRQ65 reprograms the gene expression patterns associated with systemic response to potentially facilitate its colonization and stimulate cell growth and plant biomass. Plant growth-promoting rhizobacteria (PGPR) carry out numerous mechanisms that enhance growth in seedlings, such as nutrient solubilization, phytohormone production, biocontrol activity, and regulation of induced systemic resistance (ISR) and acquired systemic resistance (ASR). Bacillus paralicheniformis TRQ65 is a biological and plant growth-promoting bacterium isolated from wheat (Triticum turgidum subsp. durum) rhizosphere. In this study, we performed a transcriptomic analysis of wheat seedlings inoculated with the native rhizobacterium Bacillus paralicheniformis TRQ65 (1 × 107 cellsâg -1 of soil) at early development stages (GS15). A morphometrical assay was carried out to confirm growth promotion and after the cultivation period, TRQ65 was re-isolated to define inoculum persistence. Inoculated seedlings showed a significant (P < 0.05) increase in shoot length (93.48%) and dry weight in both shoot (117.02%) and root (48.33%) tissues; also, the strain persisted in the soil at 1.4 × 107 UFCâg-1 of soil. A total of 228 differentially expressed genes (DEGs) (FDR < 0.05 and |log2 fold change|≥ 1.3) were observed in response to TRQ65 inoculation, of which 185 were down-regulated and 43 were up-regulated. The transcriptional patterns were characterized by the regulation of multidimensional cell growth (ROS, Ca+2 channel, and NADPH oxidases activity), suppression of defense mechanism (PR proteins, PDFs, ROS, transcription factors), induction of central stimuli receptors (RALF, WAK, MAPK), carbohydrate metabolism (invertase activity) and phytohormone-related transport (ABCG transporter and AAAP). These results suggest that B. paralicheniformis TRQ65 is a promising bioinoculant agent for increasing wheat growth and development by reprogramming ISR and ASR simultaneously, suppressing defense mechanisms and inducing central stimuli response.