Draft genome sequence of Bacillus paralicheniformis TRQ65, a biological control agent and plant growth-promoting bacterium isolated from wheat (Triticum turgidum subsp. durum) rhizosphere in the Yaqui Valley, Mexico

Comprehensive genomic analysis of Bacillus subtilis and Bacillus paralicheniformis associated with the pearl millet panicle reveals their antimicrobial potential against important plant pathogens

BACKGROUND

Plant microbiome confers versatile functional roles to enhance survival fitness as well as productivity. In the present study two pearl millet panicle microbiome member species Bacillus subtilis PBs 12 and Bacillus paralicheniformis PBl 36 found to have beneficial traits including plant growth promotion and broad-spectrum antifungal activity towards taxonomically diverse plant pathogens. Understanding the genomes will assist in devising a bioformulation for crop protection while exploiting their beneficial functional roles.

RESULTS

Two potential firmicute species were isolated from pearl millet panicles. Morphological, biochemical, and molecular characterization revealed their identities as Bacillus subtilis PBs 12 and Bacillus paralicheniformis PBl 36. The seed priming assays revealed the ability of both species to enhance plant growth promotion and seedling vigour index. Invitro assays with PBs 12 and PBl 36 showed the antibiosis effect against taxonomically diverse plant pathogens (Magnaporthe grisea; Sclerotium rolfsii; Fusarium solani; Alternaria alternata; Ganoderma sp.) of crops and multipurpose tree species. The whole genome sequence analysis was performed to unveil the genetic potential of these bacteria for plant protection. The complete genomes of PBs 12 and PBl 36 consist of a single circular chromosome with a size of 4.02 and 4.33 Mb and 4,171 and 4,606 genes, with a G + C content of 43.68 and 45.83%, respectively. Comparative Average Nucleotide Identity (ANI) analysis revealed a close similarity of PBs 12 and PBl 36 with other beneficial strains of B. subtilis and B. paralicheniformis and found distant from B. altitudinis, B. amyloliquefaciens, and B. thuringiensis. Functional annotation revealed a majority of pathway classes of PBs 12 (30) and PBl 36 (29) involved in the biosynthesis of secondary metabolites, polyketides, and non-ribosomal peptides, followed by xenobiotic biodegradation and metabolism (21). Furthermore, 14 genomic regions of PBs 12 and 15 of PBl 36 associated with the synthesis of RiPP (Ribosomally synthesized and post-translationally modified peptides), terpenes, cyclic dipeptides (CDPs), type III polyketide synthases (T3PKSs), sactipeptides, lanthipeptides, siderophores, NRPS (Non-Ribosomal Peptide Synthetase), NRP-metallophone, etc. It was discovered that these areas contain between 25,458 and 33,000 secondary metabolite-coding MiBiG clusters which code for a wide range of products, such as antibiotics. The PCR-based screening for the presence of antimicrobial peptide (cyclic lipopeptide) genes in PBs 12 and 36 confirmed their broad-spectrum antifungal potential with the presence of spoVG, bacA, and srfAA AMP genes, which encode antimicrobial compounds such as subtilin, bacylisin, and surfactin.

CONCLUSION

The combined in vitro studies and genome analysis highlighted the antifungal potential of pearl millet panicle-associated Bacillus subtilis PBs12 and Bacillus paralicheniformis PBl36. The genetic ability to synthesize several antimicrobial compounds indicated the industrial value of PBs 12 and PBl 36, which shed light on further studies to establish their action as a biostimulant for crop protection.

Survival strategies of Bacillus spp. in saline soils: Key factors to promote plant growth and health

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.

Effect of a native bacterial consortium on growth, yield, and grain quality of durum wheat (Triticum turgidum L. subsp. durum) under different nitrogen rates in the Yaqui Valley, Mexico

A field experiment was carried out to quantify the effect of a native bacterial inoculant on the growth, yield, and quality of the wheat crop, under different nitrogen (N) fertilizer rates in two agricultural seasons. Wheat was sown under field conditions at the Experimental Technology Transfer Center (CETT-910), as a representative wheat crop area from the Yaqui Valley, Sonora México. The experiment was conducted using different doses of nitrogen (0, 130, and 250 kg N ha-1) and a bacterial consortium (BC) (Bacillus subtilis TSO9, B. cabrialesii subsp. tritici TSO2T, B. subtilis TSO22, B. paralicheniformis TRQ65, and Priestia megaterium TRQ8). Results showed that the agricultural season affected chlorophyll content, spike size, grains per spike, protein content, and whole meal yellowness. The highest chlorophyll and Normalized Difference Vegetation Index (NDVI) values, as well as lower canopy temperature values, were observed in treatments under the application of 130 and 250 kg N ha-1 (the conventional Nitrogen dose). Wheat quality parameters such as yellow berry, protein content, Sodium dodecyl sulfate (SDS)-Sedimentation, and whole meal yellowness were affected by the N dose. Moreover, the application of the native bacterial consortium, under 130 kg N ha-1, resulted in a higher spike length and grain number per spike, which led to a higher yield (+1.0 ton ha-1 vs. un-inoculated treatment), without compromising the quality of grains. In conclusion, the use of this bacterial consortium has the potential to significantly enhance wheat growth, yield, and quality while reducing the nitrogen fertilizer application, thereby offering a promising agro-biotechnological alternative for improving wheat production.

Microbial inoculants with higher capacity to colonize soils improved wheat drought tolerance

Microbial inoculants have gained increasing attention worldwide as an eco-friendly solution for improving agriculture productivity. Several studies have demonstrated their potential benefits, such as enhanced resistance to drought, salinity, and pathogens. However, the beneficial impacts of inoculants remain inconsistent. This variability is attributed to limited knowledge of the mechanisms by which microbial inoculants affect crop growth and a lack of ecological characteristics of these inoculants that limit our ability to predict their beneficial effects. The first important step is believed to be the evaluation of the inoculant's ability to colonize new habitats (soils and plant roots), which could provide crops with beneficial functions and improve the consistency and efficiency of the inoculants. In this study, we aimed to investigate the impact of three microbial inoculants (two bacterial: P1 and P2, and one fungal: P3) on the growth and stress responses of three wheat varieties in two different soil types under drought conditions. Furthermore, we investigated the impact of microbial inoculants on soil microbial communities. Plant biomass and traits were measured, and high-throughput sequencing was used to characterize bulk and rhizosphere soil microbiomes after exposure to drought stress. Under drought conditions, plant shoot weight significantly increased (11.37%) under P1 treatments compared to uninoculated controls. In addition, total nitrogen enzyme activity increased significantly under P1 in sandy soil but not in clay soil. Importantly, network analyses revealed that P1, consisting of Bacillus paralicheniformis and Bacillus subtilis, emerged as the keystone taxa in sandy soil. Conversely, P2 and P3 failed to establish as keystone taxa, which may explain their insignificant impact on wheat performance under drought conditions. In conclusion, our study emphasizes the importance of effective colonization by microbial inoculants in promoting crop growth under drought conditions. Our findings support the development of microbial inoculants that robustly colonize plant roots for improved agricultural productivity.

Screening, Identification, and Growth Promotion of Antagonistic Endophytes Associated with Chenopodium quinoa Against Quinoa Pathogens

Fungal disease is one of the important reasons for crop yield reduction. Isolation of important endophytes with biocontrol and growth-promoting effects is of great significance for the exploitation of beneficial microbial resources and the biological control of crop fungal diseases. In this study, endophytes from roots, stems, and leaves of quinoa at different growth and development stages were isolated and purified; then the antagonistic activity and growth-promoting characteristics of antagonistic endophytes were determined. Finally, the antagonistic endophytes were identified by morphological characteristics and ITS/16S rRNA sequence analysis. Our results showed that 122 endophytic fungi and 371 endophytic bacteria were isolated from quinoa, of which three endophytic fungi and seven endophytic bacteria were screened that had inhibitory activity against quinoa pathogenic fungi. Most of the antagonistic strains could produce indole-3 acetic acid and had the ability to dissolve organic phosphorus. In addition, the bacterial suspension of endophytic bacteria had the ability to promote the seed germination and plant growth of quinoa. The endophytic fungi with antagonistic activity were identified as Penicillium raperi and P. pulvillorum; the endophytic bacteria were identified as Bacillus paralicheniformis, B. tequilensis, and B. velezensis, respectively. The strains of quinoa endophytes in this study can provide rich microbial resources and a theoretical basis for biological control of plant fungal diseases and agricultural production.

Detection of the Microbial Composition of Some Commercial Fermented Liquid Products via Metagenomic Analysis

The fermented liquid sector is developing all over the world due to its contribution to health. Our study has contributed to the debate about whether industrially manufactured fermented liquids live up to their claims by analyzing pathogens and beneficial bacteria using a 16S rRNA sequencing technique called metagenomic analysis. Paenibacillus, Lentibacillus, Bacillus, Enterococcus, Levilactobacillus, and Oenococcus were the most abundant bacterial genera observed as potential probiotics. Pseudomonas stutzeri, Acinetobacter, and Collimonas, which have plant-growth-promoting traits, were also detected. The fact that we encounter biocontroller bacteria that promote plant growth demonstrates that these organisms are widely used in foods and emphasizes the necessity of evaluating them in terms of public health. Their potential applications in agriculture may pose a danger to food hygiene and human health in the long term, so our data suggest that this should be evaluated.

Native Bacillus paralicheniformis isolate as a potential agent for phytopathogenic nematodes control

Phytopathogenic nematodes (PPNs) are responsible for substantial damages within agricultural crops worldwide which can be controlled employing beneficial microorganisms and/or their metabolites in an ecofriendly way. Nevertheless, the success of the control regards not only on the virulence of the strains or the toxicity of their metabolites but also on their ability to colonize and remain in the rhizospheric environment, particularly in those crops affected by abiotic stresses promoted by the climate change. Consequently, the bioprospection of beneficial microorganisms able to control PPNs and to thrive in adverse conditions has attracted attention. On this way, deserts are perfect ecological niches to isolate microorganisms adapted to harsh enviroments. The purpose of this research was to isolate and characterize bacteria from rhizospheric soil samples collected in the Northwestern Desert of Mexico with potential for PPNs control. As first screening, secretomes of each isolate were tested in vitro for nematicidal activity (NA). Then, activities from secretomes and endospores from the selected isolate were confirmed in vivo assays. From 100 thermotolerant isolates, the secretome of the isolate identified as Bacillus paralicheniformis TB197 showed the highest NA (>95%) against Meloidogyne incognita, both in vitro and in vivo tests, suppressing infections caused by M. enterolobii in tomato crops, too. In open field tests, the endospores of TB197 strain showed a reduction of 81% in the infection severity caused by M. enterolobii (p ≤ 0.05), while the galling index (GI) was reduced 84% (p ≤ 0.05) in tomato greenhouse-tests. Also, a reduction of the root necrosis (81%) caused by Radopholus similis in banana plantations (p ≤ 0.05), compared to the control was observed. Owing to their efficacy in controlling PPNs infections, the endospores and secondary metabolites of B. paralicheniformis TB197 strain could be used in bionematicidal formulations.

Microencapsulation of Bacillus Strains for Improving Wheat (Triticum turgidum Subsp. durum) Growth and Development

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 + TE3^T 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.

Current advances and research prospects for agricultural and industrial uses of microbial strains available in world collections

Microorganisms are an important component of the ecosystem and have an enormous impact on human lives. Moreover, microorganisms are considered to have desirable effects on other co-existing species in a variety of habitats, such as agriculture and industries. In this way, they also have enormous environmental applications. Hence, collections of microorganisms with specific traits are a crucial step in developing new technologies to harness the microbial potential. Microbial culture collections (MCCs) are a repository for the preservation of a large variety of microbial species distributed throughout the world. In this context, culture collections (CCs) and microbial biological resource centres (mBRCs) are vital for the safeguarding and circulation of biological resources, as well as for the progress of the life sciences. Ex situ conservation of microorganisms tagged with specific traits in the collections is the crucial step in developing new technologies to harness their potential. Type strains are mainly used in taxonomic study, whereas reference strains are used for agricultural, biotechnological, pharmaceutical research and commercial work. Despite the tremendous potential in microbiological research, little effort has been made in the true sense to harness the potential of conserved microorganisms. This review highlights (1) the importance of available global microbial collections for man and (2) the use of these resources in different research and applications in agriculture, biotechnology, and industry. In addition, an extensive literature survey was carried out on preserved microorganisms from different collection centres using the Web of Science (WoS) and SCOPUS. This review also emphasizes knowledge gaps and future perspectives. Finally, this study provides a critical analysis of the current and future roles of microorganisms available in culture collections for different sustainable agricultural and industrial applications. This work highlights target-specific potential microbial strains that have multiple important metabolic and genetic traits for future research and use.

Pangenomes-identified singletons for designing specific primers to identify bacterial strains in a plant growth-promoting consortium

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 TE3^T, Priestia megaterium TRQ8, and Bacillus paralicheniformis TRQ65, a promising beneficial bacterial consortium for wheat.

METHODS AND RESULTS

The identification of singletons of TE3^T, 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 TE3^T, 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.

Draft Genome Sequence of Bacillus paralicheniformis Strain GSFE7, a Halotolerant Plant Growth-Promoting Bacterial Endophyte Isolated from Cultivated Saline Areas of the Dead Sea Region

Here, we report the draft genome sequence of Bacillus paralicheniformis strain GSFE7, which was isolated from saline fields near the Dead Sea region. The genome was 4,452,800 bp in size and contained 4,382 coding sequences. Several genes were predicted to be involved in auxin production, nitrogen fixation, phosphate mobilization, and putative production of siderophores and antibiotics such as bacitracin, butirosin, and fengycin.

Production of a high molecular weight levan by Bacillus paralicheniformis, an industrially and agriculturally important isolate from the buffalo grass rhizosphere

A new exopolysaccharide (EPS) producing Gram-positive bacterium was isolated from the rhizosphere of Bouteloua dactyloides (buffalo grass) and its EPS product was structurally characterized. The isolate, designated as LB1-1A, was identified as Bacillus paralicheniformis based on 16S rRNA gene sequence and phylogenetic tree analysis. The EPS produced by LB1-1A was identified as a levan, having β(2 → 6) linked backbone with β(2 → 1) linkages at the branch points (4.66%). The isolate LB1-1A yielded large amount (~ 42 g/l) of levan having high weight average molecular weight (Mw) of 5.517 × 10⁷ Da. The relatively low degree of branching and high molecular weight of this levan makes B. paralicheniformis LB1-1A a promising candidate for industrial applications.

Draft genome sequence of Bacillus sp. strain FSQ1, a biological control agent against white mold in common bean (Phaseolus vulgaris L.)

•

Bacillus sp. FSQ1 was isolated from the rhizosphere of the common bean (Phaseolus vulgaris L.).

•

Bacillus sp. FSQ1 can inhibit the growth of Sclerotinia sclerotiorum.

•

The draft genome of strain Bacillus sp. FSQ1 consists of 3598,499 bp; 925,913 bp N50; 2 L50; 33 contigs; 97 RNAs and 3908 predicted CDS.

•

The GC content in the draft genome of Bacillus sp. FSQ1 is 43.0%.

•

Based on genome mining, potential metabolites involved in the biocontrol activity of strain Bacillus sp. FSQ1 are rhizocticin A and bacillibactin.

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.

Transcriptional regulation of cell growth and reprogramming of systemic response in wheat (Triticum turgidum subsp. durum) seedlings by Bacillus paralicheniformis TRQ65

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 cells∙g ^-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 UFC∙g^-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.

Bacillus tequilensis strain 'UPMRB9' improves biochemical attributes and nutrient accumulation in different rice varieties under salinity stress

Soil salinity exert negative impacts on agricultural production and regarded as a crucial issue in global wetland rice production (Oryza sativa L.). Indigenous salt-tolerant plant growth-promoting rhizobacteria (Bacillus sp.) could be used for improving rice productivity under salinity stress. This study screened potential salt-tolerant plant growth-promoting rhizobacteria (PGPR) collected from coastal salt-affected rice cultivation areas under laboratory and glasshouse conditions. Furthermore, the impacts of these PGPRs were tested on biochemical attributes and nutrient contents in various rice varieties under salt stress. The two most promising PGPR strains, i.e., 'UPMRB9' (Bacillus tequilensis 10b) and 'UPMRE6' (Bacillus aryabhattai B8W22) were selected for glasshouse trial. Results indicated that 'UPMRB9' improved osmoprotectant properties, i.e., proline and total soluble sugar (TSS), antioxidant enzymes like superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT). Moreover, 'UPMRB9' inoculated rice plants accumulated higher amount of nitrogen and calcium in tissues. Therefore, the indigenous salt-tolerant PGPR strain 'UPMRB9' could be used as a potential bio-augmentor for improving biochemical attributes and nutrient uptake in rice plants under salinity stress. This study could serve as a preliminary basis for future large-scale trials under glasshouse and field conditions.

Genomic insights into biocontrol potential of Bacillus stercoris LJBS06

Bacillus spp. have been widely reported with the ability to control plant diseases. In this work, we analyzed the whole genome of LJBS06, which was isolated from grapevine rhizosphere soil. In view of physiological and biochemical characteristics, genome data, and phylogenetic analysis of 16S rRNA, LJBS06 was affiliated with Bacillus stercoris. LJBS06 showed antagonistic activities against a variety of plant pathogens. The inhibition rate of Magnaporthe oryzae was up to 75.05% and the inhibition rates of Colletotrichum gloeosporioides, Coniothyrium diplodiella, and Botrytis cinerea were all above 50% in the plate assays. The genome of LJBS06 had a 4,154,362-bp circular chromosome, with an average GC content of 43.96%, containing an 82,935-bp plasmid with a GC content of 35.18%. The circular chromosome of LJBS06 contained 4231 protein-coding genes, 30 rRNA genes, and 87 tRNA genes, including genes related to the synthesis of plant defense-related enzymes and the promotion of plant growth. Meanwhile, 11 gene clusters involved in biosynthesis of secondary metabolites were present in the genome of LJBS06. In conclusion, our findings indicated that LJBS06 strain had the necessary genetic machinery to control plant pathogens and provided insights for future studies of the biocontrol mechanisms of B. stercoris LJBS06.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-03000-6.

COLMENA: A Culture Collection of Native Microorganisms for Harnessing the Agro-Biotechnological Potential in Soils and Contributing to Food Security

COLMENA is a microbial culture collection dedicated to the characterization, classification, preservation, and transferal of native microorganisms isolated from various agro-systems and other ecosystems in Mexico. This collection aims to protect microbial diversity, reducing soil degradation, but also exploiting its agro-biotechnological potential. So far, COLMENA has isolated and cryopreserved soil microorganisms from different crops in two major agricultural regions in Mexico, the Yaqui Valley, Sonora, and the Fuerte Valley, Sinaloa. COLMENA has specialized in the identification and characterization of microbial strains with metabolic capacities related to the promotion of plant growth and the biocontrol of phytopathogens. Thus, COLMENA has identified several promising plant growth-promoting microbial (PGPM) strains due to their metabolic and genetic potentials and their beneficial effects in vivo and field trials. These findings demonstrate the biotechnological potential of these strains for their future use in profitable agricultural alternatives focused on enhancing global food security. To share the knowledge and results of the COLMENA team’s scientific research, a virtual platform was created, where the database of the studied and preserved microorganisms is available to professionals, researchers, agricultural workers, and anyone who is interested.

Draft genome sequence of plastic degrading Bacillus sp. AIIW2 isolated from the Arabian ocean

The endemic spread of plastic in the environment requires urgent need of a sustainable approach. Marine microbes found to have vast bioactivity and play a central role in biogeochemical cycling in the ocean; however, very few of them had been explored for biochemical cycling or plastic degradation. In the present study, we report the draft genome sequence of marine Bacillus sp. AIIW2 which was found to utilize plastic as a carbon source. The Bacillus sonorensis SRCM101395 was used as a reference genome for mapping the reads. The genome size of strain AIIW2 was approximately 4.4 Mb and composed of 4737 coding sequences with 45.7% G + C contents. The whole genome comparison of strain AIIW2 with three closest Bacillus strains showed strain specificity, the 16S ribosomal RNA sequence shows 99.93% similarity with Bacillus paralicheniformis KJ-16^T (KY694465). This genome data would provide the genetic basis in developing plastic bioremediation approaches and discover the enzymes pertinent in the biodegradation processes.

Plant growth-promoting bacterial endophytes as biocontrol agents of pre- and post-harvest diseases: Fundamentals, methods of application and future perspectives

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.

Evaluation of plant growth promotion properties and induction of antioxidative defense mechanism by tea rhizobacteria of Darjeeling, India

A total of 120 rhizobacteria were isolated from seven different tea estates of Darjeeling, West Bengal, India. Based on a functional screening of in vitro plant growth-promoting (PGP) activities, thirty potential rhizobacterial isolates were selected for in-planta evaluation of PGP activities in rice and maize crops. All the thirty rhizobacterial isolates were identified using partial 16S rRNA gene sequencing. Out of thirty rhizobacteria, sixteen (53.3%) isolates belong to genus Bacillus, five (16.6%) represent genus Staphylococcus, three (10%) represent genus Ochrobactrum, and one (3.3%) isolate each belongs to genera Pseudomonas, Lysinibacillus, Micrococcus, Leifsonia, Exiguobacterium, and Arthrobacter. Treatment of rice and maize seedlings with these thirty rhizobacterial isolates resulted in growth promotion. Besides, rhizobacterial treatment in rice triggered enzymatic [ascorbate peroxidase (APX), catalase (CAT), chitinase, and phenylalanine ammonia-lyase (PAL)], and non-enzymatic [proline and polyphenolics] antioxidative defense reactions indicating their possible role in the reduction of reactive oxygen species (ROS) burden and thereby priming of plants towards stress mitigation. To understand such a possibility, we tested the effect of rhizobacterial consortia on biotic stress tolerance of rice against necrotrophic fungi, Rhizoctonia solani AG1-IA. Our results indicated that the pretreatment with rhizobacterial consortia increased resistance of the rice plants towards the common foliar pathogen like R. solani AG1-IA. This study supports the idea of the application of plant growth-promoting rhizobacterial consortia in sustainable crop practice through the management of biotic stress under field conditions.

Biocontrol of Alternaria alternata and Fusarium oxysporum by Trichoderma asperelloides and Bacillus paralicheniformis in tomato plants

The objective of this work was to evaluate the effectiveness of the putative biocontrol agents (PBA) Bacillus paralicheniformis and Trichoderma asperelloides in vitro and in vivo to control two of the most important tomato plant diseases: vascular wilt (Fusarium oxysporum) and early blight (Alternaria alternata). The assessment of the in vitro interactions between the PBA and the phytopathogenic fungi was performed by dual confrontation assays. The biocontrol effectiveness of the individual and combined PBA treatments towards individual phytopathogen inoculations was evaluated in tomato plants. T. asperelloides was able to exert an outstanding mycoparasitic effect on both phytopathogenic fungi in the in vitro tests by hyphal strangulation and penetration. In addition, the individual PBA treatments were effective in the biocontrol of A. alternata and F. oxysporum in tomato plants reducing the plant disease severity in more than 53.8 and 66.7% for each of the pathogens, respectively. On the other hand, the combined use of the tested strains showed similar effectiveness in the biocontrol of A. alternata, but no synergism was observed. In addition, it was concluded that B. paralicheniformis protected the plants from the attack of A. alternata through the induction of the systemic resistance of the plant. This study demonstrated the effectiveness of the individual and combined use of the strains tested for the biocontrol of A. alternata and F. oxysporum in tomato plants.