Exploring the Potentials of Lysinibacillus sphaericus ZA9 for Plant Growth Promotion and Biocontrol Activities against Phytopathogenic Fungi

Regulatory Players in Mycorrhizal-Bacterial-Plant Interactions

Mycorrhizae contribute significantly for plant growth and development, often providing nutrients such as phosphate and nitrogen, while also enhancing stress tolerance and resistance against phytopathogens. Plant symbiotic mycorrhizal networks harbor bacterial communities that aid mycorrhizal functions and augment plant nutrition and development. Various bacterial associations of mycorrhiza bring forth advantageous traits to mycorrhizal symbiosis and host colonization, which involves a wide range of signaling and regulatory molecules. These regulatory molecules play an important role in adapting and responding to new microenvironments with different hosts through the production of metabolites and expression of favorable genes. Small molecular components such as noncoding RNA (miRNA and sRNA) are also involved in the regulation and adaptation to these microenvironments. Regulatory pathways involving protein kinases play an important role in the tripartite association of bacteria and mycorrhizal fungi with plants, and the subsequent promotion of symbiotic interactions. This mini-review highlights potential bacterial regulatory candidates which can influence mycorrhiza-plant interactions to significantly benefit plant growth and development. An understanding of these bacterial regulatory mechanisms may suggest new strategies for knowledge-based application in crop productivity improvement programs.

Unlocking Nature's Microbial Defenders: Genetic Mechanisms and Potential Against Monilinia spp. Pathogens

Monilinia spp., which causes brown rot, is one of the most damaging pathogens in stone fruits. Researchers are exploring epiphytic and endophytic microorganisms with the potential to suppress pathogens, control pathogenic microorganisms, and/or promote plant growth. In this study, microorganisms with antagonistic activity against three Monilinia species were isolated from plum orchard soil and plum fruits. Antagonism tests in vitro showed strong antagonistic properties of six strains of bacteria and two yeast-like fungi against M. fructigena, M. fructicola, and M. laxa, with growth inhibition from 45.5 to 84.6%. The antagonists were identified and characterized at the genetic level using whole genome sequencing (WGS). Genes involved in antibiotic resistance, virulence, secondary metabolite synthesis, and plant growth promotion were identified and characterized through genome mapping, gene prediction, and annotation. None of the microorganisms studied were predicted to be pathogenic to humans. The results of this study indicate that the bacteria Bacillus pumilus, B. velezensis, two strains of Lysinibacillus agricola, Pseudomonas chlororaphis isolated from stone fruit orchard soil, and the yeast-like fungus Aureobasidium pullulans, isolated from plums, are promising candidates for the biological control of Monilinia spp.

Genome mining reveals the biosynthetic potential of a novel Lysinibacillus zambalensis sp. nov., isolated from a hyperalkaline spring

A novel bacterium, designated as strain M3T, was isolated from a hyperalkaline spring in the Philippines and identified as a new species within the genus Lysinibacillus through 16 S rRNA gene sequence and genomic analyses. Although strain M3T shared a high 16 S rRNA gene sequence similarity (> 98.7%) with many Lysinibacillus species, the digital DNA-DNA hybridization and orthologous average nucleotide identity values between strain M3T and its closet relative, Lysinibacillus xylanilyticus DSM 23,493T, were 41.2% and 90.6%, respectively-both below the established threshold for prokaryotic species delineation. Genome mining of the 5.3 Mbp-draft genome of strain M3T revealed eight biosynthetic gene clusters, which shared little sequence similarity with characterized clusters, suggesting the potential for encoding novel specialized metabolites. The cells of strain M3T were Gram-stain-positive, aerobic, rod-shaped, non-motile, and capable of endospore formation. Optimum growth was observed at 30 °C, pH 8.0, and 0.5% (w/v) NaCl. The major respiratory quinone was menaquinone-7, and the predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, and two unknown phospholipids. Its fatty acid profile showed an elevated level of iso-C15:0, and the peptidoglycan type was determined to be A4α (L-Lys-D-Asp). This study contributes to the growing database and understanding of the genus and aims to help drive future research on the bioactive potential of the genus. Lysinibacillus zambalensis sp. nov. is proposed with strain M3T as the type strain (= TISTR 10640T = BIOTECH 10973T).

Macronutrients-availing microbiomes: biodiversity, mechanisms, and biotechnological applications for agricultural sustainability

Nitrogen, phosphorus, and potassium are the three most essential micronutrients which play major roles in plant survivability by being a structural or non-structural component of the cell. Plants acquire these nutrients from soil in the fixed (NO3¯, NH4+) and solubilized forms (K+, H2PO4- and HPO42-). In soil, the fixed and solubilized forms of nutrients are unavailable or available in bare minimum amounts; therefore, agrochemicals were introduced. Agrochemicals, mined from the deposits or chemically prepared, have been widely used in the agricultural farms over the decades for the sake of higher production of the crops. The excessive use of agrochemicals has been found to be deleterious for humans, as well as the environment. In the environment, agrochemical usage resulted in soil acidification, disturbance of microbial ecology, and eutrophication of aquatic and terrestrial ecosystems. A solution to such devastating agro-input was found to be substituted by macronutrients-availing microbiomes. Macronutrients-availing microbiomes solubilize and fix the insoluble form of nutrients and convert them into soluble forms without causing any significant harm to the environment. Microbes convert the insoluble form to the soluble form of macronutrients (nitrogen, phosphorus, and potassium) through different mechanisms such as fixation, solubilization, and chelation. The microbiomes having capability of fixing and solubilizing nutrients contain some specific genes which have been reported in diverse microbial species surviving in different niches. In the present review, the biodiversity, mechanism of action, and genomics of different macronutrients-availing microbiomes are presented.

Application of Biochar-Immobilized Bacillus megaterium for Enhancing Phosphorus Uptake and Growth in Rice

Phosphorus (P) is an essential nutrient for rice growth, and the presence of phosphate-solubilizing bacteria (PSB) is an effective means to increase soil P content. However, the direct application of PSB may have minimal significance due to their low survival in soil. Biochar serves as a carrier that enhances microbial survival, and its porous structure and surface characteristics ensure the adsorption of Bacillus megaterium. Inoculating rice husk biochar-immobilized with Bacillus megaterium (BMB) resulted in dissolved inorganic and organic P levels of 39.55 and 31.97 mL L-1, respectively. Subsequently, rice pot experiments were conducted to investigate the response of soil microbial P mobilization and P uptake in rice to fertilizer inputs. The organic fertilizer (OF) combined with BMB treatment (MOF) showed the highest soil available phosphorus (AP) at 38 days, with a value of 7.83 mg kg-1, as well as increased the pqqC abundance while decreasing the abundance of phoD bacterial communities compared with the control. Furthermore, the bioavailable P reservoir (H2O-Pi and NaHCO3-Pi) in soil was greatly increased through the fertilizer input and microbial turnover, with the highest H2O-Pi (3.66 mg kg-1) in OF treatment and the highest NaHCO3-Pi (52.65 mg kg-1) in MOF treatment. Additionally, carbon utilization analysis was applied using the commercial Biolog system, revealing that the MOF treatment significantly increased the utilization of carbohydrates, polymers, and amino acid carbon sources. Moreover, compared to the control, MOF treatment significantly increased the shoot (0.469%) and root P (0.516%) content while promoting root development and thereby supporting rice growth. Our study demonstrates that the MOF treatment displayed higher P levels in both soil and rice plants, providing a theoretical basis for further understanding the role of biochar-based bacterial agents in rice P management.

Diversity of culturable bacterial isolates and their potential as antimicrobial against human pathogens from Afar region, Ethiopia

Antimicrobial resistance is a growing global concern exacerbated by the scarcity of new medications and resistance to current antibiotics. Microbes from unexplored habitats are promising sources of natural products to combat this challenge. This study aimed to isolate bacteria producing secondary metabolites and assess their antimicrobial efficacy against human pathogens. Soil and liquid samples were collected from Afar region, Ethiopia. Bacterial isolates were obtained using standard serial dilution techniques. Antimicrobial activity was evaluated using agar plug and well diffusion methods. matrix-assisted laser desorption/ionization time-of-flight-mass spectrometry (MALDI-TOF MS) and whole-genome sequencing (WGS) were conducted for the isolate exhibiting the highest antimicrobial activity. Secondary metabolites were extracted and analyzed using gas chromatography-mass spectra (GC-MS). In this study, 301 bacteria isolates were identified, of which 68 (22.6%) demonstrated antagonistic activity against at least one reference pathogen. Whole-genome sequencing revealed that Sl00103 belongs to the genus Bacillus, designated as Bacillus sp. Sl00103. The extract of Sl00103 showed zones of inhibition ranging between 17.17 ± 0.43 and 26.2 ± 0.4 mm against bacterial pathogens and 19.5 ± 0.44 to 21.0 ± 1.01 mm against Candida albicans. GC-MS analysis of ethyl acetate and n-hexane extracts identified major compounds including (R,R)-butane-2,3-diol; 3-isobutylhexahydropyrrolo[1,2a] pyrazine-1,4-dione; cyclo(L-prolyl-L-valine); and tetradecanoic acid, 12-methyl-, methyl ester; hexadecanoic acid, methyl ester among other. In conclusion, this study isolated several promising bacterial strains from the Afar region in Ethiopia, with strain Sl00103 (Bacillus sp. Sl00103) demonstrating notable antimicrobial and antioxidant activities and warranting further studies.

IMPORTANCE

Antimicrobial resistance (AMR) is an escalating global health threat affecting humans, animals, and the environment, underscoring the urgent need for alternative pathogen control methods. Natural products, particularly secondary metabolites from bacteria, continue to be a vital source of antibiotics. However, microbial habitats and metabolites in Africa remain largely unexplored. In this study, we isolated and screened bacteria from Ethiopia's Afar region, characterized by extreme conditions like high temperatures, volcanic activity, high salinity, and hot springs to identify potential bioactive compounds. We discovered diverse bacterial isolates with antimicrobial activity against various pathogens, including strain Sl00103 (Bacillus sp. Sl00103), which demonstrated significant antimicrobial and antioxidant activities. GC-MS analysis identified several antimicrobial compounds, highlighting strain Sl00103 as a promising source of secondary metabolites with potential pharmaceutical applications and warranting further investigation.

Influence of combined application of tetracycline and streptomycin on microbial diversity and function in rice soil

A microcosm experiment was performed to quantify the residues of antibiotics [tetracycline (TC), streptomycin (STR), and streptocycline (STC; a mixture of TC and STR)] in rice soil and to assess their impact on microbial community structure and function using Illumina-MiSeq metagenomic analysis. Antibiotics were applied at half the recommended dose (0.5RD), recommended dose (RD), and double the recommended dose (2RD). At RD, TC was degraded in soil within 9 days of its application, whereas it took 21 days for STR and STC to degrade below limit of quantification (LOQ) level. The residue data were fitted in decay models, and half-lives (DT50) were 46.5-53.3 h and 177.6-198 h for TC and STR, respectively. Soil enzyme activities (dehydrogenase, β-glucosidase, fluorescein diacetate hydrolase, acid phosphatase, alkaline phosphatase) were negatively affected in the antibiotic-treated soil. Targeted metagenomic analysis showed that the major bacterial phyla such as Chloroflexi, Actinobacteria, Planctomycetes, Crenarchaeota, and Gemmatimonadetes were suppressed by antibiotic treatments as compared to control. Shannon, Simpson, ACE, and Chao1 diversity indices showed that bacterial diversity decreased with the application of antibiotics, and decrease in bacterial diversity was more prominent in case of STC as compared to TC and STR. Overall, the combination of antibiotics negatively affected the soil microbial community structure and function in comparison to their individual application.

Protorhabditis nematodes and pathogen-antagonistic bacteria interactively promote plant health

BACKGROUND

Fertilization practices control bacterial wilt-causing Ralstonia solanacearum by shaping the soil microbiome. This microbiome is the start of food webs, in which nematodes act as major microbiome predators. However, the multitrophic links between nematodes and the performance of R. solanacearum and plant health, and how these links are affected by fertilization practices, remain unknown.

RESULTS

Here, we performed a field experiment under no-, chemical-, and bio-organic-fertilization regimes to investigate the potential role of nematodes in suppressing tomato bacterial wilt. We found that bio-organic fertilizers changed nematode community composition and increased abundances of bacterivorous nematodes (e.g., Protorhabditis spp.). We also observed that pathogen-antagonistic bacteria, such as Bacillus spp., positively correlated with abundances of bacterivorous nematodes. In subsequent laboratory and greenhouse experiments, we demonstrated that bacterivorous nematodes preferentially preyed on non-pathogen-antagonistic bacteria over Bacillus. These changes increased the performance of pathogen-antagonistic bacteria that subsequently suppressed R. solanacearum.

CONCLUSIONS

Overall, bacterivorous nematodes can reduce the abundance of plant pathogens, which might provide a novel protection strategy to promote plant health. Video Abstract.

Effect of a Bacillus velezensis and Lysinibacillus fusiformis-based biofertilizer on phosphorus acquisition and grain yield of soybean

Introduction

Phosphate-solubilizing bacteria that function through acidification (organic acid synthesis) or mineralization (production of enzymes such as phytase and phosphatases) have been explored as a biotechnological alternative to enhance plant access to phosphorus (P) retained in organic and inorganic forms in agricultural soils. This study tested the hypothesis that applying a biofertilizer composed of a recognized phosphate-solubilizing bacterium (Bacillus velezensis - endophytic strain BVPS01) and an underexplored plant growth-promoting bacterium (Lysinibacillus fusiformis - endophytic strain BVPS02) would improve the growth and grain yield of Glycine max L. plants.

Methods

Initial in vitro tests assessed the functional traits of these bacteria, and a mix of strains BVPS01 and BVPS02 was produced and tested under field conditions to evaluate its agronomic efficiency.

Results

The results confirmed the hypothesis that the tested biofertilizer enhances the agronomic performance of G. max plants in the field. The B. velezensis strain (BVPS01) was found to be more effective than the L. fusiformis strain (BVPS02) in solubilizing phosphates via the phosphatase enzyme production pathway, indicated by the expression of the phoC and phoD genes. In contrast, L. fusiformis was more effective in solubilizing phosphates through organic acid and phytase-related pathways, in addition to synthesizing indole-3-acetic acid and increasing the mitotic index in the root meristem of G. max plants. These strains exhibited biological compatibility, and the formulated product based on these rhizobacteria enhanced root development and increased the number of nodules and flowers, positively affecting 1000-grain weight, grain yield, and grain P content.

Discussion

Thus, the tested biofertilizer demonstrated potential to improve root growth and increase both the yield and quality of soybean crops, making it a sustainable and low-cost strategy.

Impact of Intercropping Five Medicinal Plants on Soil Nutrients, Enzyme Activity, and Microbial Community Structure in Camellia oleifera Plantations

Intercropping medicinal plants plays an important role in agroforestry that can improve the physical, chemical, and biological fertility of soil. However, the influence of intercropping medicinal plants on the Camellia oleifera soil properties and bacterial communities remains elusive. In this study, five intercropping treatment groups were set as follows: Curcuma zedoaria/C. oleifera (EZ), Curcuma longa/C. oleifera (JH), Clinacanthus nutans/C. oleifera (YDC), Fructus Galangae/C. oleifera (HDK), and Ficus simplicissima/C. oleifera (WZMT). The soil chemical properties, enzyme activities, and bacterial communities were measured and analyzed to evaluate the effects of different intercropping systems. The results indicated that, compared to the C. oleifera monoculture group, YDC and EZ showed noticeable impacts on the soil chemical properties with a significant increase in total nitrogen (TN), nitrate nitrogen (NN), available nitrogen (AN), available phosphorus (AP), and available potassium (AK). Among them, the content of TN and AK in the rhizosphere soil of Camellia oleifera in the YDC intercropping system was the highest, which was 7.82 g/kg and 21.94 mg/kg higher than CK. Similarly, in the EZ intercropping system, the content of NN and OM in the rhizosphere soil of Camellia oleifera was the highest, which was higher than that of CK at 722.33 mg/kg and 2.36 g/kg, respectively. Curcuma longa/C. oleifera (JH) and Clinacanthus nutans/C. oleifera (YDC) had the most effect on soil enzyme activities. Furthermore, YDC extensively increased the activities of hydrogen peroxide and acid phosphatase enzymes; the increase was 2.27 mg/g and 3.21 mg/g, respectively. While JH obviously increased the urease activity, the diversity of bacterial populations in the rhizosphere soil of the intercropping plants decreased, especially the Shannon index of YDC and HDK. Compared with the monoculture group, the bacterial community abundance and structure of JH and YDC were quite different. The relative abundance of Actinobacteriota and Firmicutes was increased in YDC, and that of Acidobacteriota and Myxococcota was increased in JH. According to the redundancy analysis (RDA), pH, total potassium, and soil catalase activity were identified as the main factors influencing the microbial community structure of the intercropping systems. In conclusion, intercropping with JH and YDC increased the relative abundance of the dominant bacterial communities, improved the microbial community structure, and enhanced the soil nutrients and enzyme activities. Therefore, in the future, these two medicinal plants can be used for intercropping with C. oleifera.

Exploring Pathogen Presence Prediction in Pastured Poultry Farms through Transformer-Based Models and Attention Mechanism Explainability

In this study, we explore how transformer models, which are known for their attention mechanisms, can improve pathogen prediction in pastured poultry farming. By combining farm management practices with microbiome data, our model outperforms traditional prediction methods in terms of the F1 score-an evaluation metric for model performance-thus fulfilling an essential need in predictive microbiology. Additionally, the emphasis is on making our model's predictions explainable. We introduce a novel approach for identifying feature importance using the model's attention matrix and the PageRank algorithm, offering insights that enhance our comprehension of established techniques such as DeepLIFT. Our results showcase the efficacy of transformer models in pathogen prediction for food safety and mark a noteworthy contribution to the progress of explainable AI within the biomedical sciences. This study sheds light on the impact of effective farm management practices and highlights the importance of technological advancements in ensuring food safety.

Comparative genomics reveals insights into the potential of Lysinibacillus irui as a plant growth promoter

Members of the genus Lysinibacillus attract attention for their mosquitocidal, bioremediation, and plant growth-promoting abilities. Despite this interest, comprehensive studies focusing on genomic traits governing plant growth and stress resilience in this genus using whole-genome sequencing are still scarce. Therefore, we sequenced and compared the genomes of three endophytic Lysinibacillus irui strains isolated from Canary Island date palms with the ex-type strain IRB4-01. Overall, the genomes of these strains consist of a circular chromosome with an average size of 4.6 Mb and a GC content of 37.2%. Comparative analysis identified conserved gene clusters within the core genome involved in iron acquisition, phosphate solubilization, indole-3-acetic acid biosynthesis, and volatile compounds. In addition, genome analysis revealed the presence of genes encoding carbohydrate-active enzymes, and proteins that confer resistance to oxidative, osmotic, and salinity stresses. Furthermore, pathways of putative novel bacteriocins were identified in all genomes. This illustrates possible common plant growth-promoting traits shared among all strains of L. irui. Our findings highlight a rich repertoire of genes associated with plant lifestyles, suggesting significant potential for developing inoculants to enhance plant growth and resilience. This study is the first to provide insights into the overall genomic signatures and mechanisms of plant growth promotion and biocontrol in the genus Lysinibacillus. KEY POINTS: • Pioneer study in elucidating plant growth promoting in L. irui through comparative genomics. • Genome mining identified biosynthetic pathways of putative novel bacteriocins. • Future research directions to develop L. irui-based biofertilizers for sustainable agriculture.

Short-term high-temperature pretreated compost increases its application value by altering key bacteria phenotypes

Short-term high-temperature pretreatment can effectively shorten the maturity period of organic waste composting and improve the fertilizer efficiency and humification degree of products. To investigate the effect and mechanism of the end products on the saline-alkali soil improvement and plant growth, the short-term high-temperature pretreatment composting (SHC) and traditional composting (STC) were separately blended with saline-alkali soil in a ratio of 0-40 % to establish a soil-fertilizer blended matrix for cultivating Lolium perenne L. The pot experiments combined with principal component analysis showed Lolium perenne L. planted in 20 % SHC-blended saline-alkali soil had the best growth effect, and its biomass, chlorophyll content, and plant height were 109-113 % higher than STC. The soil physicochemical property analysis showed that SHC and STC increased the soil nutrient content, humification degree, and enzyme activity at any blending ratio. The microbial analysis showed that 20 % SHC in the saline-alkali soil stimulated the growth of functional microorganisms and the addition of SHC promoted the sulfur cycle, nitrogen fixation, and carbon metabolism in the soil-plant system. The correlation analysis showed that pH; nutrient contents; and urease, catalase, sucrase, and phosphatase activities in the saline-alkali soil were significantly correlated with plant growth indexes (p < 0.05). Georgenia and norank_f__Fodinicurvataceae had a stronger correlation with four types of enzyme activities (p < 0.01). SHC improved the saline-alkali soil and promoted plant growth by adjusting soil pH, increasing soil nutrients, and influencing soil enzyme activity and dominant flora. This study provides a theoretical basis for applying SHC products in soil improvement.

Influence of Soil Phosphate on Rhizobacterial Performance in Affecting Wheat Yield

As a primary nutrient in agricultural soils, phosphorus plays a crucial but growth-limiting role for plants due to its complex interactions with various soil elements. This often results in excessive phosphorus fertilizer application, posing concerns for the environment. Agri-research has therefore shifted focus to increase fertilizer-use efficiency and minimize environmental impact by leveraging plant growth-promoting rhizobacteria. This study aimed to evaluate the in-field incremental effect of inorganic phosphate concentration (up to 50 kg/ha/P) on the ability of two rhizobacterial isolates, Lysinibacillus sphaericus (T19), Paenibacillus alvei (T29), from the previous Breedt et al. (Ann Appl Biol 171:229-236, 2017) study on maize in enhancing the yield of commercially grown Duzi® cultivar wheat. Results obtained from three seasons of field trials revealed a significant relationship between soil phosphate concentration and the isolates' effectiveness in improving wheat yield. Rhizospheric samples collected at flowering during the third season, specifically to assess phosphatase enzyme activity at the different soil phosphate levels, demonstrated a significant decrease in soil phosphatase activity when the phosphorus rate reached 75% for both isolates. Furthermore, in vitro assessments of inorganic phosphate solubilization by both isolates at five increments of tricalcium phosphate-amended Pikovskaya media found that only isolate T19 was capable of solubilizing tricalcium at concentrations exceeding 3 mg/ml. The current study demonstrates the substantial influence of inorganic phosphate on the performance of individual rhizobacterial isolates, highlighting that this is an essential consideration when optimizing these isolates to increase wheat yield in commercial cultivation.

Biosynthesis of novel desferrioxamine derivatives requires unprecedented crosstalk between separate NRPS-independent siderophore pathways

Iron is essential to many biological processes but its poor solubility in aerobic environments restricts its bioavailability. To overcome this limitation, bacteria have evolved a variety of strategies, including the production and secretion of iron-chelating siderophores. Here, we describe the discovery of four series of siderophores from Streptomyces ambofaciens ATCC23877, three of which are unprecedented. MS/MS-based molecular networking revealed that one of these series corresponds to acylated desferrioxamines (acyl-DFOs) recently identified from S. coelicolor. The remaining sets include tetra- and penta-hydroxamate acyl-DFO derivatives, all of which incorporate a previously undescribed building block. Stable isotope labeling and gene deletion experiments provide evidence that biosynthesis of the acyl-DFO congeners requires unprecedented crosstalk between two separate non-ribosomal peptide synthetase (NRPS)-independent siderophore (NIS) pathways in the producing organism. Although the biological role(s) of these new derivatives remain to be elucidated, they may confer advantages in terms of metal chelation in the competitive soil environment due to the additional bidentate hydroxamic functional groups. The metabolites may also find application in various fields including biotechnology, bioremediation, and immuno-PET imaging.IMPORTANCEIron-chelating siderophores play important roles for their bacterial producers in the environment, but they have also found application in human medicine both in iron chelation therapy to prevent iron overload and in diagnostic imaging, as well as in biotechnology, including as agents for biocontrol of pathogens and bioremediation. In this study, we report the discovery of three novel series of related siderophores, whose biosynthesis depends on the interplay between two NRPS-independent (NIS) pathways in the producing organism S. ambofaciens-the first example to our knowledge of such functional cross-talk. We further reveal that two of these series correspond to acyl-desferrioxamines which incorporate four or five hydroxamate units. Although the biological importance of these novel derivatives is unknown, the increased chelating capacity of these metabolites may find utility in diagnostic imaging (for instance, 89Zr-based immuno-PET imaging) and other applications of metal chelators.

Metabolomics Reveals Lysinibacillus capsici TT41-Induced Metabolic Shifts Enhancing Drought Stress Tolerance in Kimchi Cabbage (Brassica rapa L. subsp. pekinensis)

Climate change has increased variable weather patterns that affect plants. To address these issues, we developed a microbial biocontrol agent against drought stress in kimchi cabbage (Brassica rapa L. subsp. pekinensis). We selected three bacterial strains (Leifsonia sp. CS9, Bacillus toyonensis TSJ7, and Lysinibacillus capsici TT41) because they showed a survival rate of up to 50% and good growth rate when treated with 30% PEG 6000. The three strains were treated with kimchi cabbage to confirm their enhanced drought stress resistance under non-watering conditions. Among the three strains, the TT41 treated group showed a significant increase in various plant parameters compared with the negative control on the 7th day. We performed extensive profiling of primary and secondary metabolites from kimchi cabbage and the TT41 strain. Multivariate and pathway analyses revealed that only the TT41 group clustered with the well-watered group and showed almost the same metabolome on the 7th day. When treated with TT41, lactic acid was identified as an indicator metabolite that significantly improved drought stress tolerance. Furthermore, lactic acid treatment effectively induced drought stress tolerance in kimchi cabbage, similar to that achieved with the TT41 strain.

Correlation Between Microbial Community and Hatching Failure in Loggerhead Sea Turtle Caretta caretta

Microbial communities provide essential information about host ecology and could be helpful as a tool to improve species conservation efforts. However, microbes can also infect and compromise the host development process and viability. Caretta caretta is the most widespread marine turtle species in the Mediterranean basin and is the only species of sea turtle nesting along the Italian coasts. Little is known about the microbiota composition of the nest of sea turtles and its correlation with hatching failures. In this study, the microbial composition of two nests of C. caretta featuring different rates of hatching success from a nesting beach in Lampedusa (Italy) was analyzed and compared. The bacterial community was determined using culture-dependent methods and next-generation sequencing based on 16S rRNA gene metabarcoding analysis. Our results showed five dominant bacterial phyla (Proteobacteria, Bacteroidetes, Actinobacteria, Verrucomicrobia, and Firmicutes) and indicated different bacterial families (Pseudomonadaceae and Brucellaceae) as likely causes of hatching failures. Besides, our findings demonstrated the nests' active role in modulating the sand's bacterial communities. This study suggests microbiological analysis could be a valuable tool in monitoring nests to take preventive actions and reduce hatching failures.

Disclosing the native blueberry rhizosphere community in Portugal-an integrated metagenomic and isolation approach

Backgorund

The production of red fruits, such as blueberry, has been threatened by several stressors from severe periods of drought, nutrient scarcity, phytopathogens, and costs with fertilization programs with adverse consequences. Thus, there is an urgent need to increase this crop's resilience whilst promoting sustainable agriculture. Plant growth-promoting microorganisms (PGPMs) constitute not only a solution to tackle water and nutrient deficits in soils, but also as a control against phytopathogens and as green compounds for agricultural practices.

Methods

In this study, a metagenomic approach of the local fungal and bacterial community of the rhizosphere of Vaccinium corymbosum plants was performed. At the same time, both epiphytic and endophytic microorganisms were isolated in order to disclose putative beneficial native organisms.

Results

Results showed a high relative abundance of Archaeorhizomyces and Serendipita genera in the ITS sequencing, and Bradyrhizobium genus in the 16S sequencing. Diversity analysis disclosed that the fungal community presented a higher inter-sample variability than the bacterial community, and beta-diversity analysis further corroborated this result. Trichoderma spp., Bacillus spp., and Mucor moelleri were isolated from the V. corymbosum plants.

Discussion

This work revealed a native microbial community capable of establishing mycorrhizal relationships, and with beneficial physiological traits for blueberry production. It was also possible to isolate several naturally-occurring microorganisms that are known to have plant growth-promoting activity and confer tolerance to hydric stress, a serious climate change threat. Future studies should be performed with these isolates to disclose their efficiency in conferring the needed resilience for this and several crops.

Lysinibacillus spp.: an IAA-producing endospore forming-bacteria that promotes plant growth

Lysinibacillus is a bacterial genus that has generated recent interest for its biotechnological potential in agriculture. Strains belonging to this group are recognized for their mosquitocidal and bioremediation activity. However, in recent years some reports indicate its importance as plant growth promoting rhizobacteria (PGPR). This research sought to provide evidence of the PGP activity of Lysinibacillus spp. and the role of the indole-3-acetic acid (IAA) production associated with this activity. Twelve Lysinibacillus spp. strains were evaluated under greenhouse conditions, six of which increased the biomass and root architecture of corn plants. In most cases, growth stimulation was evident at 10⁸ CFU/mL inoculum concentration. All strains produced IAA with high variation between them (20-70 µg/mL). The bioinformatic identification of predicted genes associated with IAA production allowed the detection of the indole pyruvic acid pathway to synthesize IAA in all strains; additionally, genes for a tryptamine pathway were detected in two strains. Extracellular filtrates from all strain's cultures increased the corn coleoptile length in an IAA-similar concentration pattern, which demonstrates the filtrates had an auxin-like effect on plant tissue. Five of the six strains that previously showed PGPR activity in corn also promoted the growth of Arabidopsis thaliana (col 0). These strains induced changes in root architecture of Arabidopsis mutant plants (aux1-7/axr4-2), the partial reversion of mutant phenotype indicated the role of IAA on plant growth. This work provided solid evidence of the association of Lysinibacillus spp. IAA production with their PGP activity, which constitutes a new approach for this genus. These elements contribute to the biotechnological exploration of this bacterial genus for agricultural biotechnology.

Bioremediation of the herbicide glyphosate in polluted soils by plant-associated microbes

Most productive lands worldwide base their crop production on the use of glyphosate (GLY)-resistant plants, and consequently, widespread use of this herbicide has led to environmental issues that need to be solved. Soil bioremediation technologies based on degradation of GLY by microorganisms are strategies that have been considered useful to solve this environmental problem. Recently, a further step has been taken considering the use of bacteria that interact with plants, either alone or both bacteria and plant together, for the removal of GLY herbicide. Plant-interacting microorganisms with plant growth-promoting traits can also enhance plant growth and contribute to successful bioremediation strategies.

Lysinibacilli: A Biological Factories Intended for Bio-Insecticidal, Bio-Control, and Bioremediation Activities

Microbes are ubiquitous in the biosphere, and their therapeutic and ecological potential is not much more explored and still needs to be explored more. The bacilli are a heterogeneous group of Gram-negative and Gram-positive bacteria. Lysinibacillus are dominantly found as motile, spore-forming, Gram-positive bacilli belonging to phylum Firmicutes and the family Bacillaceae. Lysinibacillus species initially came into light due to their insecticidal and larvicidal properties. Bacillus thuringiensis, a well-known insecticidal Lysinibacillus, can control many insect vectors, including a malarial vector and another, a Plasmodium vector that transmits infectious microbes in humans. Now its potential in the environment as a piece of green machinery for remediation of heavy metal is used. Moreover, some species of Lysinibacillus have antimicrobial potential due to the bacteriocin, peptide antibiotics, and other therapeutic molecules. Thus, this review will explore the biological disease control abilities, food preservative, therapeutic, plant growth-promoting, bioremediation, and entomopathogenic potentials of the genus Lysinibacillus.

The Antibacterial, Antitumor Activities, and Bioactive Constituents’ Identification of Alectra sessiliflora Bacterial Endophytes

Due to increased antimicrobial resistance against current drugs, new alternatives are sought. Endophytic bacteria associated with medicinal plants are recognized as valuable sources of novel secondary metabolites possessing antimicrobial, antitumor, insecticidal, and antiviral activities. In this study, five bacterial endophytes were isolated and identified from the medicinal plant, Alectra sessiliflora, and their antibacterial and antitumor activities were investigated. In addition, the crude extracts of the endophytes were analyzed using gas chromatography (GC) coupled with time-of-flight mass spectrometry (TOF-MS). The identified bacterial endophytes belong to three genera viz Lysinibacillus, Peribacillus, and Bacillus, with the latter as the dominant genus with three species. Ethyl acetate extracts from the endophytes were used for antimicrobial activity against eleven pathogenic strains through minimum inhibitory concentration (MIC). The antitumor activity against the Hela cervical, Hek 293 kidney, and A549 lung carcinoma cells was determined by the MTS [3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxy-phenyl)-2-(4-sulfophenyl)-2H-tetrazolium] assay. Lysinibacillus sp. strain AS_1 exhibited broad antibacterial activity against the pathogenic strains with MIC values ranging from 4 to 8 mg/ml, while Bacillus sp. strain AS_3 displayed MIC of 0.25 mg/ml. Crude extracts of Lysinibacillus sp. strain AS_1, Peribacillus sp. strain AS_2, and Bacillus sp. strain AS_3 showed growth inhibition of more than 90% against all the cancer cell lines at a concentration of 1,000 μg/ml. Untargeted secondary metabolite profiling of the crude extracts revealed the presence of compounds with reported biological activity, such as antimicrobial, antioxidant, anti-inflammatory, antitumor, and antidiabetic properties. This study reported for the first time, bacterial endophytes associated with A. sessiliflora with antibacterial and antitumor activities.

Lysinibacillus Isolate MK212927: A Natural Producer of Allylamine Antifungal ‘Terbinafine’

Resistance to antifungal agents represents a major clinical challenge, leading to high morbidity and mortality rates, especially in immunocompromised patients. In this study, we screened soil bacterial isolates for the capability of producing metabolites with antifungal activities via the cross-streak and agar cup-plate methods. One isolate, coded S6, showed observable antifungal activity against Candida (C.) albicans ATCC 10231 and Aspergillus (A.) niger clinical isolate. This strain was identified using a combined approach of phenotypic and molecular techniques as Lysinibacillus sp. MK212927. The purified metabolite displayed fungicidal activity, reserved its activity in a relatively wide range of temperatures (up to 60 °C) and pH values (6–7.8) and was stable in the presence of various enzymes and detergents. As compared to fluconazole, miconazole and Lamisil, the minimum inhibitory concentration of the metabolite that showed 90% inhibition of the growth (MIC₉₀) was equivalent to that of Lamisil, half of miconazole and one fourth of fluconazole. Using different spectroscopic techniques such as FTIR, UV spectroscopy, 1D NMR and 2D NMR techniques, the purified metabolite was identified as terbinafine, an allylamine antifungal agent. It is deemed necessary to note that this is the first report of terbinafine production by Lysinibacillus sp. MK212927, a fast-growing microbial source, with relatively high yield and that is subject to potential optimization for industrial production capabilities.

Prevalence of toxigenic fungi and mycotoxins in Arabic coffee (Coffea arabica): Protective role of traditional coffee roasting, brewing and bacterial volatiles

Fungal infection and synthesis of mycotoxins in coffee leads to significant economic losses. This study aimed to investigate the prevalence of toxigenic fungi, their metabolites, and the effect of traditional roasting and brewing on ochratoxin A (OTA) and aflatoxins (AFs) contents of naturally contaminated coffee samples. In addition, in vivo biocontrol assays were performed to explore the antagonistic activities of Bacillus simplex 350–3 (BS350-3) on the growth and mycotoxins synthesis of Aspergillus ochraceus and A. flavus. The relative density of A. niger, A. flavus, Penicillium verrucosum and A. carbonarius on green coffee bean was 60.82%, 7.21%, 3.09% and 1.03%, respectively. OTA contents were lowest in green coffee beans (2.15 μg/kg), followed by roasted (2.76 μg/kg) and soluble coffee (8.95 μg/kg). Likewise, AFs levels were highest in soluble coffee (90.58 μg/kg) followed by roasted (33.61 μg/kg) and green coffee (9.07 μg/kg). Roasting naturally contaminated coffee beans at three traditional methods; low, medium and high, followed by brewing resulted in reduction of 58.74% (3.50 μg/kg), 60.88% (3.72 μg/kg) and 64.70% (4.11 μg/kg) in OTA and 40.18% (34.65 μg/kg), 47.86% (41.17 μg/kg) and 62.38% (53.73 μg/kg) AFs contents, respectively. Significant inhibitions of AFs and OTA synthesis by A. flavus and A. carbonarius, respectively, on infected coffee beans were observed in presence of Bacillus simplex BS350-3 volatiles. Gas chromatography mass spectrochemistry (GC-MS/MS) analysis of head-space BS350-3 volatiles showed quinoline, benzenemethanamine and 1-Octadecene as bioactive antifungal molecules. These findings suggest that marketed coffee samples are generally contaminated with OTA and AFs, with a significant level of roasted and soluble coffee contaminated above EU permissible limits for OTA. Further, along with coffee roasting and brewing; microbial volatiles can be optimized to minimize the dietary exposure to mycotoxins.

Plant Triterpenoids Regulate Endophyte Community to Promote Medicinal Plant Schisandra sphenanthera Growth and Metabolites Accumulation

Beneficial interactions between endophytes and plants are critical for plant growth and metabolite accumulation. Nevertheless, the secondary metabolites controlling the feedback between the host plant and the endophytic microbial community remain elusive in medicinal plants. In this report, we demonstrate that plant-derived triterpenoids predominantly promote the growth of endophytic bacteria and fungi, which in turn promote host plant growth and secondary metabolite productions. From culturable bacterial and fungal microbial strains isolated from the medicinal plant Schisandra sphenanthera, through triterpenoid-mediated screens, we constructed six synthetic communities (SynComs). By using a binary interaction method in plates, we revealed that triterpenoid-promoted bacterial and fungal strains (TPB and TPF) played more positive roles in the microbial community. The functional screening of representative strains suggested that TPB and TPF provide more beneficial abilities to the host. Moreover, pot experiments in a sterilized system further demonstrated that TPB and TPF play important roles in host growth and metabolite accumulation. In summary, these experiments revealed a role of triterpenoids in endophytic microbiome assembly and indicated a strategy for constructing SynComs on the basis of the screening of secondary metabolites, in which bacteria and fungi join forces to promote plant health. These findings may open new avenues towards the breeding of high yielding and high metabolite-accumulating medicinal plants by exploiting their interaction with beneficial endophytes.

The Impact of the Inoculation of Phosphate-Solubilizing Bacteria Pantoea agglomerans on Phosphorus Availability and Bacterial Community Dynamics of a Semi-Arid Soil

The bacterial genus Pantoea has been widely evaluated as promising bacteria to increase phosphorus (P) availability in soil. The aim of this study was to characterize the phosphate solubilizing (PS) activity of a Pantoea agglomerans strain and to evaluate the impact of its application in a semi-arid soil on phosphate availability and structure of the bacterial communities as a whole. An incubation experiment under close-to-natural soil environmental conditions was conducted for 15 days at 30 °C. High-throughput sequencing of the bacterial 16S rRNA gene was used to characterize and to compare the bacterial community structure of P. agglomerans-inoculated soil with non-inoculated control. Furthermore, a qPCR-based method was developed for detection and quantification of the functional genes related to the expression of mineral phosphate solubilization (MPS) phenotype in P. agglomerans. The results showed that in vitro solubilization of Ca3(PO4)2 by P. agglomerans strain was very efficient (980 mg/L), and it was associated with a drop in pH due to the secretion of gluconic acid; these changes were concomitant with the detection of gdh and pqqC genes. Moreover, P. agglomerans inoculum application significantly increased the content of available P in semi-arid soil by 69%. Metagenomic analyses showed that P. agglomerans treatment modified the overall edaphic bacterial community, significantly impacting its structure and composition. In particular, during P. agglomerans inoculation the relative abundance of bacteria belonging to Firmicutes (mainly Bacilli class) significantly increased, whereas the abundance of Actinobacteria together with Acidobacteria and Chloroflexi phyla decreased. Furthermore, genera known for their phosphate solubilizing activity, such as Aneurinibacillus, Lysinibacillus, Enterococcus, and Pontibacter, were exclusively detected in P. agglomerans-treated soil. Pearson's correlation analysis revealed that changes in soil bacterial community composition were closely affected by soil characteristics, such as pH and available P. This study explores the effect of the inoculation of P. agglomerans on the bacterial community structure of a semi-arid soil. The effectiveness in improving the phosphate availability and modification in soil bacterial community suggested that P. agglomerans represent a promising environmental-friendly biofertilizer in arid and semi-arid ecosystems.

Bacterial communities associated with sugarcane under different agricultural management exhibit a diversity of plant growth-promoting traits and evidence of synergistic effect

Plant-associated microbiomes have been a target of interest for the prospection of microorganisms, which may be acting as effectors to increase agricultural productivity. For years, the search for beneficial microorganisms has been carried out from the characterization of functional traits of growth-promotion using tests with a few isolates. However, eventually, the expectations with positive results may not be realized when the evaluation is performed in association with plants. In our study, we accessed the cultivable sugarcane microbiome under two conditions of agronomic management: organic and conventional. From the use of a new customized culture medium, we recovered 944 endophytic and epiphytic bacterial communities derived from plant roots, stalks, leaves, and rhizospheric soil. This could be accomplished by using a large-scale approach, initially performing an in planta (Cynodon dactylon) screening process of inoculation to avoid early incompatibility. The inoculation was performed using the bacterial communities, considering that in this way, they could act synergistically. This process resulted in 38 candidate communities, 17 of which had higher Indole-3-acetic acid (IAA) production and phosphate solubilization activity and, were submitted to a new in planta test using Brachiaria ruziziensis and quantification of functional traits for growth-promotion and physiological tests. Enrichment analysis of selected communities has shown that they derived mainly from epiphytic populations of sugarcane stalks under conventional management. The sequencing of the V3-V4 region of the 16S rRNA gene revealed 34 genera and 24 species distributed among the phylum Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. We also observed a network of genera in these communities where the genus Chryseobacterium stands out with a greater degree of interaction, indicating a possible direct or indirect role as a keystone taxon in communities with plant-growth promotion capacities. From the results achieved, we can conclude that the approach is useful in the recovery of a set of sugarcane bacterial communities and that there is, evidence of synergistic action providing benefits to plants, and that they are compatible with plants of the same family (Poaceae). Thus, we are reporting the beneficial bacterial communities identified as suitable candidates with rated potential to be exploited as bioinoculants for crops.

Rhizobacterial consortium mediated aroma and yield enhancement in basmati and non-basmati rice (Oryza sativa L.)

Basmati and non-basmati rice varieties are commercially important. Aromatic rice varieties are low yielding and recently depletion in aroma is observed due to the shift towards modern agriculture. Therefore, it is necessary to restore the aroma and increase the yield through sustainable agriculture. The use of microbial bioinoculants is one of the promising ways to achieve these targets. With these objectives, rhizospheric bacterial strains Enterobacter hormaechei (AM122) and Lysinibacillus xylanilyticus (DB25) having the property of synthesizing 2-acetyl-1-pyrroline (2AP) were isolated from the rhizosphere of two aromatic rice varieties, Ambemohar-157 and Dehradun Basmati respectively and their effect on plant growth, aroma and yield enhancement under mono-inoculation and consortium conditions was analyzed. The bacterial inoculum in consortium resulted in significant improvement in vegetative growth, yield and 2AP content over mono inoculation and control. The study highlights the potential of E. hormaechei and L. xylanilyticus in plant growth, yield and aroma enhancement in basmati and non-basmati rice varieties. These strains can be taken up further for developing a commercial bioformulation.

Optimized Production of the Allylamine Antifungal "Terbinafine" by Lysinibacillus Isolate MK212927 Using Response Surface Methodology

Purpose

We aimed to optimize the factors affecting the production of the allylamine antifungal, terbinafine, by Lysinibacillus isolate MK212927, a natural producer of this broad-spectrum fungicidal compound.

Methods

We employed a central composite design to optimize the five most important variables influencing the production of terbinafine which were carbon source, nitrogen source, temperature, pH and agitation.

Results

The optimum conditions were found to be starch 5 g/L, ammonium chloride 5 g/L, temperature 32°C, agitation 150 rpm and pH 7. The actual response (inhibition zone diameter) was highly comparable to the value predicted by the model, indicating a valid model. Using the standard calibration curve of terbinafine, the optimized conditions resulted in an increase in the antifungal metabolite production (terbinafine) by about 1.6-fold (1814.662 µg/mL compared to 1165.550 µg/mL under standardized conditions).

Conclusion

This is the first report, to the best of our knowledge, on optimized production of terbinafine by Lysinibacillus species. Hence, these findings may be useful as baseline data for scaling up the production of terbinafine from a natural microbial source.

Culturable Bacterial Community on Leaves of Assam Tea (Camellia sinensis var. assamica) in Thailand and Human Probiotic Potential of Isolated Bacillus spp

Assam tea plants (Camellia sinensis var. assamica) or Miang are found in plantations and forests of Northern Thailand. Leaf fermentation has been performed for centuries, but little information is available about their associated microbial community. One hundred and fifty-seven bacterial isolates were isolated from 62 Assam tea leaf samples collected from 6 provinces of Northern Thailand and classified within the phyla of Firmicutes, Actinobacteria, and Proteobacteria. Phayao and Phrae provinces exhibited the highest and the lowest bacterial diversities, respectively. The bacterial community structural pattern demonstrated significant differences between the west and the east sides. Since some Bacillus spp. have been reported to be involved in fermented Miang, Bacillus spp. isolated in this study were chosen for further elucidation. Bacillus siamensis ML122-2 exhibited a growth inhibitory effect against Staphylococcus aureus ATCC 25923 and MRSA DMST 20625, and the highest survival ability in simulated gastric and intestinal fluids (32.3 and 99.7%, respectively), autoaggregation (93.2%), cell surface hydrophobicity (50.0%), and bacterial adherence with Vero cells (75.8% of the control Lactiplantibacillusplantarum FM03-1). This B. siamensis ML122-2 is a promising probiotic to be used in the food industry and seems to have potential antibacterial properties relevant for the treatment of antibiotic-resistant infections.

Genetically modified entomopathogenic bacteria, recent developments, benefits and impacts: A review

Entomopathogenic bacteria (EPBs), insect pathogens that produce pest-specific toxins, are environmentally-friendly alternatives to chemical insecticides. However, the most important problem with EPBs application is their limited field stability. Moreover, environmental factors such as solar radiation, leaf temperature, and vapor pressure can affect the pathogenicity of these pathogens and their toxins. Scientists have conducted intensive research to overcome such problems. Genetic engineering has great potential for the development of new engineered entomopathogens with more resistance to adverse environmental factors. Genetically modified entomopathogenic bacteria (GM-EPBs) have many advantages over wild EPBs, such as higher pathogenicity, lower spraying requirements and longer-term persistence. Genetic manipulations have been mostly applied to members of the bacterial genera Bacillus, Lysinibacillus, Pseudomonas, Serratia, Photorhabdus and Xenorhabdus. Although many researchers have found that GM-EPBs can be used safely as plant protection bioproducts, limited attention has been paid to their potential ecological impacts. The main concerns about GM-EPBs and their products are their potential unintended effects on beneficial insects (predators, parasitoids, pollinators, etc.) and rhizospheric bacteria. This review address recent update on the significant role of GM-EPBs in biological control, examining them through different perspectives in an attempt to generate critical discussion and aid in the understanding of their potential ecological impacts.

In vitro antibacterial activities and molecular characterization of bacterial species isolated from farmlands against selected pathogens

This study aims to screen bacterial isolates from Olabisi Onabanjo University Farmland for antibacterial activity against pathogenic microorganisms. Agar well diffusion method was used. Isolates were identified molecularly. Chi-square test revealed significant association between isolates, antibacterial activity with likelihood p-value = 0.000 and 5% significant level. Six among thirty-five isolates exhibited antibacterial activity against the test pathogenic species. A greater antibacterial activity (50 % inhibition) was observed in Lysinibacillus sphearicus strain PRE16. It inhibited the growth of Bacillus subtilis, Staphylococcus aureus and Escherichia coli by 23.00 ± 2.00, 18.00 ± 2.00 and 20.00 ± 4.00 respectively. DNA sequencing revealed antagonist isolates as Bacillus sp. BCN2, Brochothrix thermosphacta strain P30C4, Bacillus aryabhattai strain KNUC205, Alcaligenes faecalis strain KEM24, Bacillus arsenicus strain CSD05 and Lysinibacillus sphaericus strain PRE16. Phylogenetic analysis revealed close relatedness of most isolates with Bacillus species strains. These strains are suggested to be effective for the discovery of new antibacterial agents.

Characterization of plant growth-promoting bacteria associated with avocado trees (Persea americana Miller) and their potential use in the biocontrol of Scirtothrips perseae (avocado thrips)

Plants interact with a great variety of microorganisms that inhabit the rhizosphere or the epiphytic and endophytic phyllosphere and that play critical roles in plant growth as well as the biocontrol of phytopathogens and insect pests. Avocado fruit damage caused by the thrips species Scirtothrips perseae leads to economic losses of 12–51% in many countries. In this study, a screening of bacteria associated with the rhizosphere or endophytic phyllosphere of avocado roots was performed to identify bacterial isolates with plant growth-promoting activity in vitro assays with Arabidopsis seedlings and to assess the biocontrol activity of the isolates against Scirtothrips perseae. The isolates with beneficial, pathogenic and/or neutral effects on Arabidopsis seedlings were identified. The plant growth-promoting bacteria were clustered in two different groups (G1 and G3B) based on their effects on root architecture and auxin responses, particularly bacteria of the Pseudomonas genus (MRf4-2, MRf4-4 and TRf2-7) and one Serratia sp. (TS3-6). Twenty strains were selected based on their plant growth promotion characteristics to evaluate their potential as thrips biocontrol agents. Analyzing the biocontrol activity of S. perseae, it was identified that Chryseobacterium sp. shows an entomopathogenic effect on avocado thrips survival. Through the metabolic profiling of compounds produced by bacteria with plant growth promotion activity, bioactive cyclodipeptides (CDPs) that could be responsible for the plant growth-promoting activity in Arabidopsis were identified in Pseudomonas, Serratia and Stenotrophomonas. This study unravels the diversity of bacteria from the avocado rhizosphere and highlights the potential of a unique isolate to achieve the biocontrol of S. perseae.

Synergistic effect of Lysinibacillus sphaericus and glyphosate on temephos-resistant larvae of Aedes aegypti

BACKGROUND

Glyphosate-based herbicides are one of the most commonly used compounds to control perennial weeds around the world. This compound is very persistent in the environment and tends to filter into aquatic ecosystems, affecting non-target species such as mosquito larvae. Aedes aegypti mosquitoes are vectors of multiple arboviruses such as dengue and Zika. Glyphosate can be degraded into non-harmful environmental compounds by Lysinibacillus sphaericus, a spore forming bacterium which can also kill Ae. aegypti larvae. In this study, we assessed the effect of glyphosate concentrations, typically used in Colombia, on the entomopathogenic activity of L. sphaericus against Ae. aegypti larvae.

METHODS

Bioassays and toxicity curves were performed to compare the larval mortality between different treatments with and without bacteria and glyphosate (Roundup 747®). Larvae were exposed to both bacteria and glyphosate by adding the compound on chloride-free water. Comparisons were made using both probit regression and ANOVA analysis.

RESULTS

ANOVA showed a significant difference in larval mortality when adding glyphosate and L. sphaericus at the same time. Thus, a positive synergic effect on larval mortality was found when L. sphaericus and glyphosate were mixed. According to probit analysis, median lethal dose (LD50) for bacterial mixture was of 106.23 UFC/ml and for glyphosate was 2.34 g/l.

CONCLUSIONS

A positive synergic effect on the mortality of larval Ae. aegypti when exposed to L. sphaericus mixture and glyphosate was found. Molecular studies focusing on the toxin production of L. sphaericus are required to understand more about this synergistic effect.

Inoculation of Lupinus albus with the nodule-endophyte Paenibacillus glycanilyticus LJ121 improves grain nutritional quality

Metabolic changes occurring in white lupine grain were investigated in response to Plant Growth Promoting Rhizobacteria (PGPR) root inoculation under field condition. We precisely targeted lipids and phenolics changes occurring in white lupine grain in response to Pseudomonas brenneri LJ215 and/or Paenibacillus glycanilyticus LJ121 inoculation. Lipids and phenolic composition were analyzed using an Ultra High-Performance Liquid Chromatography/Tandem Mass Spectrometry Methods. As compared to grain of un-inoculated control plant, Paenibacillus glycaniliticus inoculation highly increased the total lipids content (from 232.55 in seeds of un-inoculated control plant to 944.95 mg/kg) and the relative percentage of several fatty acid such as oleic acid (+20.95%) and linoleic acid (+14.28%) and decreased the relative percentage of glycerophospholipids (- 13.11%), sterol (- 0.2% and - 0.34% for stigmasterol and campesterol, respectively) and prenol (- 17.45%) class. Paenibacillus glycaniliticus inoculation did not affect total phenolic content, while it modulated content of individual phenolic compounds and induced the accumulation of "new" phenolics compounds such as kaempferol. Paenibacillus glycanilyticus LJ121 can be a useful bio-fertilizer to enhance nutritional quality of white lupine grain.

Talaromyces variabilis interferes with Pythium aphanidermatum growth and suppresses Pythium-induced damping-off of cucumbers and tomatoes

Pythium-induced damping-off disease is a major disease limiting cucumber and tomato production in different parts of the world. The current study investigated the efficiency of Talaromyces variabilis and its bioactive metabolites in suppressing Pythium-induced damping-off of cucumbers and tomatoes. T. variabilis inhibited the in vitro growth of P. aphanidermatum in solid and liquid media. In addition, abnormalities in P. aphanidermatum hyphae were observed as a result of T. variabilis. Extracts from T. variabilis induced cellular leakage and suppressed oospore production of P. aphanidermatum. Biochemical analyses of T. variabilis metabolites showed that T. variabilis produces glucanase, cellulase and siderophores, suggesting the contribution of these metabolites in the inhibition of P. aphandermatum growth and in hyphal abnormalities. Treating cucumber seeds with spore and mycelial suspension of T. variabilis isolates led to a significant improvement in the seedling survival of P. aphanidermatum-inoculated seedlings from 18 to 52% (improvement by 34%) for isolate 48 P and from 30–66% (improvement by 36%) for isolate 28 R. Similarly, treating tomato seeds with spore and mycelial suspension of T. variabilis isolates led to a significant improvement in the seedling survival of P. aphanidermatum-inoculated seedlings from 7 to 36% (improvement by 29%) for isolate 28 R and from 20 to 64% (improvement by 44%) for isolate 48 P. Differences in the percent improvement in seedling survival between experiments may be related to difference in the efficacy of the two different isolates or their interaction with the hosts and pathogen. The use of T. variabilis in the biocontrol of Pythium-induced diseases may offer alternatives to the currently used chemical control.

Isolation, identification and plant growth promotion ability of endophytic bacteria associated with lupine root nodule grown in Tunisian soil

The present study aims to characterize nodule endophytic bacteria of spontaneous lupine plants regarding their diversity and their plant growth promoting (PGP) traits. The potential of PGPR inoculation was investigated to improve white lupine growth across controlled, semi-natural and field conditions. Lupinus luteus and Lupinus angustifolius nodules were shown inhabited by a large diversity of endophytes. Several endophytes harbor numerous plant growth promotion traits such as phosphates solubilization, siderophores production and 1-aminocyclopropane-1-carboxylate deaminase activity. In vivo analysis confirmed the plant growth promotion ability of two strains (Paenibacillus glycanilyticus LJ121 and Pseudomonas brenneri LJ215) in both sterilized and semi-natural conditions. Under field conditions, the co-inoculation of lupine by these strains increased shoot N content and grain yield by 25% and 36%, respectively. These two strains Paenibacillus glycanilyticus LJ121 and Pseudomonas brenneri LJ215 are effective plant growth-promoting bacteria and they may be used to develop an eco-friendly biofertilizer to boost white lupine productivity.

Glucose dehydrogenase gene containing phosphobacteria for biofortification of Phosphorus with growth promotion of rice

Phosphorus (P) is an essential plant nutrient, but often limited in soils for plant uptake. A major economic constraint in the rice production is excessive use of chemical fertilizers to meet the P requirement. Bioaugmentation of phosphate solubilizing rhizobacteria (PSB) can be used as promising alternative. In the present study 11 mineral PSB were isolated from Basmati rice growing areas of Pakistan. In broth medium, PSB solubilized tricalcium phosphate (27-354 μg mL^-1) with concomitant decrease in pH up to 3.6 due to the production of different organic acids, predominantly gluconic acid. Of these, 4 strains also have ability to mineralize phytate (245-412 μg mL^-1). Principle component analysis showed that the gluconic acid producing PSB strains (Acinetobacter sp. MR5 and Pseudomonas sp. MR7) have pronounced effect on grain yield (up to 55%), plant P (up to 67%) and soil available P (up to 67%), with 20% reduced fertilization. For simultaneous validation of gluconic acid production by MR5 and MR7 through PCR, new specific primers were designed to amplify gcd, pqqE, pqqC genes responsible for glucose dehydrogenase (gcd) mediated phosphate solubilization. These findings for the first time demonstrated Acinetobacter soli as potent P solubilizer for rice and expands our knowledge about genus specific pqq and gcd primers. These two gcd containing PSB Acinetobacter sp. MR5 (DSM 106631) and Pseudomonas sp. MR7 (DSM 106634) submitted to German culture collection (DSMZ), serve as global valuable pool to significantly increase the P uptake, growth and yield of Basmati rice with decreased dependence on chemical fertilizer in P deficit agricultural soils.

Amelioration of drought effects in wheat and cucumber by the combined application of super absorbent polymer and potential biofertilizer

Biofertilizer is a good substitute for chemical fertilizer in sustainable agriculture, but its effects are often hindered by drought stress. Super absorbent polymer (SAP), showing good capacity of water absorption and retention, can increase soil moisture. However, limited information is available about the efficiency of biofertilizer amended with SAP. This study was conducted to investigate the effects of synergistic application of SAP and biofertilizers (Paenibacillus beijingensis BJ-18 and Bacillus sp. L-56) on plant growth, including wheat and cucumber. Potted soil was treated with different fertilizer combinations (SAP, BJ-18 biofertilizer, L-56 biofertilizer, BJ-18 + SAP, L-56 + SAP), and pot experiment was carried out to explore its effects on viability of inoculants, seed germination rate, plant physiological and biochemical parameters, and expression pattern of stress-related genes under drought condition. At day 29 after sowing, the highest viability of strain P. beijingensis BJ-18 (264 copies ng^-1 gDNA) was observed in BJ-18 + SAP treatment group of wheat rhizosphere soil, while that of strain Bacillus sp. L-56 (331 copies ng^-1 gDNA) was observed in the L-56 + SAP treatment group of cucumber rhizosphere soil. In addition, both biofertilizers amended with SAP could promote germination rate of seeds (wheat and cucumber), plant growth, soil fertility (urease, sucrose, and dehydrogenase activities). Quantitative real-time PCR analysis showed that biofertilizer + SAP significantly down-regulated the expression levels of genes involved in ROS scavenging (TaCAT, CsCAT, TaAPX, and CsAPX2), ethylene biosynthesis (TaACO2, CsACO1, and CsACS1), stress response (TaDHN3, TaLEA, and CsLEA11), salicylic acid (TaPR1-1a and CsPR1-1a), and transcription activation (TaNAC2D and CsNAC35) in plants under drought stress. These results suggest that SAP addition in biofertilizer is a good tactic for enhancing the efficiency of biofertilizer, which is beneficial for plants in response to drought stress. To the best of our knowledge, this is the first report about the effect of synergistic use of biofertilizer and SAP on plant growth under drought stress.

Identification of Soil Bacterial Isolates Suppressing Different Phytophthora spp. and Promoting Plant Growth

Bacterial isolates obtained from the rhizosphere of Arabidopsis and a plantless compost potting mix was screened for anti-oomycete activity against Phytophthora capsici, Phytophthora citricola, Phytophthora palmivora, and Phytophthora cinnamomi. Three out of 48 isolates exhibited more than 65% inhibition against all tested Phytophthora species and were selected for further studies. These strains, named UQ154, UQ156, and UQ202, are closely related to Bacillus amyloliquefaciens, Bacillus velezensis, and Acinetobacter sp., respectively, based on 16S rDNA sequence analysis. The isolates were evaluated for their ability to fix nitrogen, solubilize phosphate, as well as for siderophore, indoleacetic acid, cell wall degrading enzymes and biofilm production. Their plant growth promoting activities were evaluated by measuring their effect on the germination percentage, root and shoot length, and seedling vigor of lettuce plants. All of these traits were significantly enhanced in plants grown from seeds inoculated with the isolates compared with control plants. Moreover, bacteria-inoculated P. capsici-infected chili plants exhibited improved productivity based on CO2 assimilation rates. Both real-time quantitative PCR and disease severity index revealed significant decreases in pathogen load in infected chili root tissues when plants were previously inoculated with the isolates. Biocontrol activity may result from the secretion of diketopiperazines as identified by Gas chromatography-mass spectrometry analysis of bacterial cultures' extracts. Collectively, this work demonstrates the potential of bacterial isolates to control Phytophthora infection and promote plant growth. They can, therefore be considered as candidate microbial biofertilizers and biopesticides.

Rice Phyllosphere Bacillus Species and Their Secreted Metabolites Suppress Aspergillus flavus Growth and Aflatoxin Production In Vitro and In Maize Seeds

The emergence of super-toxigenic strains by recombination is a risk from an intensive use of intraspecific aflatoxin (AF) biocontrol agents (BCAs). Periodical alternation with interspecific-BCAs will be safer since they preclude recombination. We are developing an AF-biocontrol system using rice-associated Bacilli reported previously (RABs). More than 50% of RABs inhibited the growth of multiple A. flavus strains, with RAB4R being the most inhibitory and RAB1 among the least. The fungistatic activity of RAB4R is associated with the lysis of A. flavus hyphal tips. In field trails with the top five fungistatic RABs, RAB4R consistently inhibited AF contamination of maize by Tox4, a highly toxigenic A. flavus strain from Louisiana corn fields. RAB1 did not suppress A. flavus growth, but strongly inhibited AF production. Total and HPLC-fractionated lipopeptides (LPs) isolated from culture filtrates of RAB1 and RAB4R also inhibited AF accumulation. LPs were stable in vitro with little loss of activity even after autoclaving, indicating their potential field efficacy as a tank-mix application. A. flavus colonization and AF were suppressed in RAB1- or RAB4R-coated maize seeds. Since RAB4R provided both fungistatic and strong anti-mycotoxigenic activities in the laboratory and field, it can be a potent alternative to atoxigenic A. flavus strains. On the other hand, RAB1 may serve as an environmentally safe helper BCA with atoxigenic A. flavus strains, due its lack of strong fungistatic and hemolytic activities.

Aspergillus terreus Inhibits Growth and Induces Morphological Abnormalities in Pythium aphanidermatum and Suppresses Pythium-Induced Damping-Off of Cucumber

The study investigated the efficacy of two isolates of Aspergillus terreus (65P and 9F) on the growth, morphology and pathogenicity of Pythium aphanidermatum on cucumber. In vitro tests showed that the two isolates inhibited the growth of P. aphanidermatum in culture. Investigating P. aphanidermatum hyphae close to the inhibition zone showed that the hyphae showed abnormal growth and loss of internal content. Treating P. aphanidermatum with the culture filtrate (CF) of A. terreus resulted in significant rise in cellular leakage of P. aphanidermatum mycelium. Testing glucanase enzyme activity by both A. terreus isolates showed a significant increase in glucanase activity. This suggests that the cell walls of Pythium, which consist of glucan, are affected by the glucanase enzyme produced by A. terreus. In addition, Aspergillus isolates produced siderephore, which is suggested to be involved in inhibition of Pythium growth. Also, the CFs of 65P and 9F isolates significantly reduced spore production by P. aphanidermatum compared to the control (P < 0.05). In bioassay tests, the two isolates of A. terreus increased the survival rate of cucumber seedlings from 10 to 20% in the control seedlings treated with P. aphanidermatum to 38-39% when the biocontrol agents were used. No disease symptoms were observed on cucumber seedlings only treated with the isolates 65P and 9F of A. terreus. In addition, the A. terreus isolates did not have any negative effects on the growth of cucumber seedlings. This study shows that isolates of A. terreus can help suppress Pythium-induced damping-off of cucumber, which is suggested to be through the effect of A. terreus and its glucanase enzyme on P. aphanidermatum mycelium.

Biocontrol of Bacterial Leaf Blight of Rice and Profiling of Secondary Metabolites Produced by Rhizospheric Pseudomonas aeruginosa BRp3

Xanthomonas oryzae pv. oryzae (Xoo) is widely prevalent and causes Bacterial Leaf Blight (BLB) in Basmati rice grown in different areas of Pakistan. There is a need to use environmentally safe approaches to overcome the loss of grain yield in rice due to this disease. The present study aimed to develop inocula, based on native antagonistic bacteria for biocontrol of BLB and to increase the yield of Super Basmati rice variety. Out of 512 bacteria isolated from the rice rhizosphere and screened for plant growth promoting determinants, the isolate BRp3 was found to be the best as it solubilized 97 μg/ mL phosphorus, produced 30 μg/mL phytohormone indole acetic acid and 15 mg/ L siderophores in vitro. The isolate BRp3 was found to be a Pseudomonas aeruginosa based on 16S rRNA gene sequencing (accession no. HQ840693). This bacterium showed antagonism in vitro against different phytopathogens including Xoo and Fusarium spp. Strain BRp3 showed consistent pathogen suppression of different strains of BLB pathogen in rice. Mass spectrometric analysis detected the production of siderophores (1-hydroxy-phenazine, pyocyanin, and pyochellin), rhamnolipids and a series of already characterized 4-hydroxy-2-alkylquinolines (HAQs) as well as novel 2,3,4-trihydroxy-2-alkylquinolines and 1,2,3,4-tetrahydroxy-2-alkylquinolines in crude extract of BRp3. These secondary metabolites might be responsible for the profound antibacterial activity of BRp3 against Xoo pathogen. Another contributing factor toward the suppression of the pathogen was the induction of defense related enzymes in the rice plant by the inoculated strain BRp3. When used as an inoculant in a field trial, this strain enhanced the grain and straw yields by 51 and 55%, respectively, over non-inoculated control. Confocal Laser Scanning Microscopy (CLSM) used in combination with immunofluorescence marker confirmed P. aeruginosa BRp3 in the rice rhizosphere under sterilized as well as field conditions. The results provide evidence that novel secondary metabolites produced by BRp3 may contribute to its activity as a biological control agent against Xoo and its potential to promote the growth and yield of Super Basmati rice.