Rhizosphere Of Tomato Plants Research Articles

Ecological Diversity of Lycopersicon esculentum (Tomato) Root Associated Plant Growth Promoting Rhizobacteria (PGPRs)

Tomato member of family Solanaceae is one amongst the foremost important vegetable crop worldwide. It has its significance due to its nutritive, therapeutic and antioxidant properties. An ecofriendly approach to improve the crop yield is the use of PGPRs which improves the growth of plant through nitrogen fixation, phosphorus solubilization and phyto-hormone production. The present study is to evaluate the biodiversity of such PGPRs and their potential role as biofertilizer for tomato crop. A total eight bacteria were isolated and purified from soil and rhizosphere of tomato plant collected from temperate and tropical rainfed regions of Pakistan including Rawalakot and Attock respectively. Soil texture of Rawalakot and Attock varied from sandy loam to loamy. Plant growth promoting traits like N2 Fixation, P-solubilization and IAA production were determined for all the eight isolates. Maximum P-solubilization was shown by isolates from Attock, AS4 (129.72 µg mL-1) and Rawalakot, RS3 (132.73 µg mL-1) and maximum IAA production was observed in Rawalakot isolates, RS2 (22.237 µg mL-1) followed by Attock isolates, AS3 (49.63 µg mL-1) and AS2 (62.86 µg mL-1). PGPRs were selected with multifunctional properties and were used in plant inoculation experiment to study enhanced growth of tomato plants. Bacterial isolates showed remarkable increase in all growth parameters as compare to uninoculated control. These PGPRs can be best developed for improved development of tomato plants with less dependence on chemical fertilizers.

First report of the nematode‐trapping fungus Arthrobotrys thaumasia in Türkiye and its biocontrol potential against Meloidogyne incognita

AbstractRoot‐knot nematodes, particularly, Meloidogyne incognita, are among the most destructive endoparasitic nematodes, infecting a diverse range of plant hosts. Nematode‐trapping fungi are known for their potential application as biological control agents against plant parasitic nematodes. In the present study, the nematode‐trapping fungus Arthrobotrys thaumasia was isolated from the rhizosphere soil of tomato plants in the West Mediterranean Region of Türkiye. Two hundred and twenty‐three tomato plant rhizosphere soil samples yielded six nematode‐trapping fungal isolates, giving an occurrence frequency of 2.69%. Using morphology and molecular marker sequences (ITS and β‐tubulin loci), the species of the fungi was confirmed to be A. thaumasia. In vitro, A. thaumasia reduced second‐stage juveniles of M. incognita by 77.5% (isolate I‐Y4‐2) and 72.5% (isolate B‐G5‐1). This is the first report on the isolation and characterization of the nematode‐trapping fungus A. thaumasia from Türkiye. Two isolates of A. thaumasia (I‐Y4‐2 and B‐G5‐1) appear to be promising biological control agents that may be utilized for controlling M. incognita‐caused root‐knot diseases.

EVALUATION OF MICROBIAL POTENTIAL OF RHIZOBACTERIAL ISOLATES ASSOCIATED WITH SPENT MUSHROOM COMPOST AGAINST BACTERIAL WILT OF TOMATO

Bacterial wilt, caused by the soil-borne pathogen Ralstonia solanacearum, poses a significant threat to tomato crops worldwide. This study aims to assess the microbial potential of rhizobacterial isolates obtained from spent mushroom compost in suppressing bacterial wilt of tomatoes. Spent mushroom compost is a byproduct of mushroom cultivation and is known to harbor diverse microbial communities with potential plant-beneficial properties. Tomato leaves that were contaminated were collected from a number of places in the Rawalpindi Area, Punjab, Pakistan. Rhizobacterial isolates were collected from the rhizosphere of tomato plants grown in the presence of spent mushroom compost. These isolates were then subjected to laboratory evaluations for their antagonistic activity against R. solanacearum. Selected rhizobacterial isolates were further characterized for their plant growth-promoting traits. The potential of these isolates to enhance tomato plant growth and confer resistance against bacterial wilt was evaluated through greenhouse experiments. Results indicated that certain rhizobacterial isolates exhibited substantial antagonistic activity against R. solanacearum. Additionally, these isolates demonstrated multiple plant growth-promoting traits, suggesting a potential dual role in both pathogen suppression and plant enhancement. Greenhouse experiments revealed a significant reduction in the incidence of bacterial wilt in tomato plants and increase in the growth promotion traits were observed while treated with the selected rhizobacterial isolates alone and in combination compared to control groups. The findings from this study highlight the promising role of rhizobacterial isolates associated with spent mushroom compost in managing bacterial wilt in tomatoes.

Nanoscale sulfur alters the bacterial and eukaryotic communities of the tomato rhizosphere and their interactions with a fungal pathogen

Nanoformulations of sulfur have demonstrated the potential to enhance plant growth and reduce disease incidence when plants are confronted with pathogens. However, the impact of nanoscale sulfur on microbial communities in close contact with the plant root, known as the rhizosphere, remain poorly characterized. In this study, we investigate the impact of three formulations of sulfur; bulk sulfur, uncoated (pristine) sulfur nanoparticles, and stearic acid coated sulfur nanoparticles, on the rhizosphere of tomato plants. Tomato plants were additionally challenged by the pathogenic fungus Fusarium oxysporum f. sp. Lycopersici. Employing bacterial 16S rRNA gene sequencing, along with recently in-house designed peptide nucleic acid clamps to facilitate the recovery of microeukaryote sequences, we performed a comprehensive survey of rhizosphere microbial populations. We found the largest influence on the composition of the rhizosphere microbiome was the presence of the fungal pathogen. However, sulfur amendments also drove state changes in the rhizosphere populations; for example, enriching the relative abundance of the plant-beneficial sulfur-oxidizing bacterium Thiobacillus. Notably, when investigating the response of the rhizosphere community to the different sulfur amendments, there was a strong interaction between the fungal pathogen and sulfur treatments. This resulted in different bacterial and eukaryotic taxa being enriched in association with the different forms of sulfur, which was dependent on the presence of the pathogen. These data point to nano formulations of sulfur exerting unique shifts in the rhizosphere community compared to bulk sulfur, particularly in association with a plant pathogen, and have implications for the sustainable use of nanoscale strategies in sustainable agriculture.

Quantifying the Respiratory Pattern of Rhizosphere Microbial Communities in Healthy and Diseased Tomato Plants Using Carbon Substrates

The sustainable production of tomatoes (Solanum lycopersicum) is important, and this can be achieved by determining the rate of respiration of microbes in the tomato plants' rhizosphere soil. This study aimed at the potential of microbes to utilize carbon substrates embedded in the rhizosphere soil thereby contributing to the healthy nature of the tomato plants. The potential soil physiochemical features and utilization of carbon substrate by soil microorganisms as a result of their respiration to reveal their functions in the ecosystem were evaluated. The soil samples were amassed from the healthy tomato plant rhizosphere, diseased tomatoes, and bulk soil in this study. The physiochemical features and carbon substrate utilization in the bulk soil samples, and rhizosphere samples of powdery diseased, and healthy tomato plants were assessed. The MicroRespTM procedure was used to determine the community-level physiological profiles (CLPP) employing fifteen (15) carbon (C) substrates selected based on their importance to microbial communities embedded in the soil samples. Our results revealed that various physiochemical properties, moisture content, water retention, and C substrates including sugar, amino acid, and carboxylic acid were greater in HR and the substrates were not significantly different (p < 0.05). The study reveals higher soil respiration in HR as a result of the microbial communities inhabiting HR utilizing more of the C-substrates. This investigation contributes to the tomato plant's healthy state as the microbial communities utilized carbon substrate compared to DR after employing the CLPP assays.

Enhancing plant defense using rhizobacteria in processing tomatoes: a bioprospecting approach to overcoming Early Blight and Alternaria toxins.

Plant growth-promoting rhizobacteria (PGPR) with antagonistic activity toward plant pathogenic fungi are valuable candidates for the development of novel plant protection products based on biocontrol activity. The very first step in the formulation of such products is to screen the potential effectiveness of the selected microorganism(s). In this study, non-pathogenic rhizobacteria were isolated from the rhizosphere of tomato plants and evaluated for their biocontrol activity against three species of mycotoxin-producing Alternaria. The assessment of their biocontrol potential involved investigating both fungal biomass and Alternaria toxin reduction. A ranking system developed allowed for the identification of the 12 best-performing strains among the initial 85 isolates. Several rhizobacteria showed a significant reduction in fungal biomass (up to 76%) and/or mycotoxin production (up to 99.7%). Moreover, the same isolates also demonstrated plant growth-promoting (PGP) traits such as siderophore or IAA production, inorganic phosphate solubilization, and nitrogen fixation, confirming the multifaceted properties of PGPRs. Bacillus species, particularly B. amyloliquefaciens and two strains of B. subtilis, showed the highest efficacy in reducing fungal biomass and were also effective in lowering mycotoxin production. Isolates such as Enterobacter ludwigii, Enterobacter asburiae, Serratia nematodiphila, Pantoea agglomerans, and Kosakonia cowanii showed moderate efficacy. Results suggest that by leveraging the diverse capabilities of different microbial strains, a consortium-based approach would provide a broader spectrum of effectiveness, thereby signaling a more encouraging resolution for sustainable agriculture and addressing the multifaceted nature of crop-related biotic challenges.

Biofilm producing probiotic bacteria enhance productivity and bioactive compounds in tomato

The aim was to increase yield and bioactive compounds in tomatoes by application of different biofilm producing plant probiotic bacteria (BPPPB). In this study, sixteen (64%) biofilm producing bacteria (BPB) were identified using 16S rRNA gene sequencing from rhizosphere of tomato plants, comprising the genera of Pseudomonas, Bacillus and Enterobacter. Examined biofilms contained secreted biomolecules including peptidoglycans, proteins, nucleic acids, polysaccharides and lipids, and cell-associated appendages like curli fimbriae. All of the BPB produced multiple probiotic traits in vitro including indole-3-acetic acid, the solubilization of P, Fe, Zn, and K, the fixation of N, and the synthesis of NH3, catalase, acetoin, protease, and cellulase. Tomato plants that have been inoculated with P. poae ESN2, B. aryabhattai ESN3, B. megaterium ESN4, E. cloacae ESN16, P. monteilii ESN26, P. putida ESN32, P. fluorescens ESN35, P. extremorientalis ESN36, and P. chlororaphis ESN37 increased biomass production (4.3–20.7% roots and 6.0–41.7% shoots), yield (4.4–69.1%), total soluble solids (11.2–33.5%), lycopene (28.5–142.8%), β-carotene (27.2–363.6%), phenolics (6.3–52%), flavonoids (10.4–69.2%), and antioxidant capacity (13.3–66.6%) over controls. This is the first report of improvements in tomato yield and bioactive compounds achieved through the application of BPPPB.

Phenotypic and Genotypic Characterization of Newly Isolated Xanthomonas euvesicatoria-Specific Bacteriophages and Evaluation of Their Biocontrol Potential

Bacteriophages have greatly engaged the attention of scientists worldwide due to the continuously increasing resistance of phytopathogenic bacteria to commercially used chemical pesticides. However, the knowledge regarding phages is still very insufficient and must be continuously expanded. This paper presents the results of the isolation, characterization, and evaluation of the potential of 11 phage isolates as natural predators of a severe phytopathogenic bacterium-Xanthomonas euvesicatoria. Phages were isolated from the rhizosphere of tomato plants with symptoms of bacterial spot. The plaque morphology of all isolates was determined on a X. euvesicatoria lawn via a plaque assay. Three of the isolates were attributed to the family Myoviridae based on TEM micrographs. All phages showed good long-term viability when stored at 4 °C and -20 °C. Three of the phage isolates possessed high stability at very low pH values. Fifty-five-day persistence in a soil sample without the presence of the specific host and a lack of lytic activity on beneficial rhizosphere bacteria were found for the phage isolate BsXeu269p/3. The complete genome of the same isolate was sequenced and analyzed, and, for the first time in this paper, we report a circular representation of a linear but circularly permuted phage genome among known X. euvesicatoria phage genomes.

Functional interplay between antagonistic bacteria and Rhizoctonia solani in the tomato plant rhizosphere.

Microbial interactions with plant roots play an imperial role in tomato plant growth and defense against the Rhizoctonia solani. This study performed a field experiment with two antagonistic bacteria (Pseudomonas and Bacillus) inoculated in healthy and Rhizoctonia solani treated soil in tomato rhizosphere to understand the metabolic pattern and microbial function during plant disease suppression. In the present study, we assessed soil and microbial enzymes, bacterial and fungal cell forming unit (CFU), and carbon utilization profiling through Bio-Eco plates of rhizoplane samples. Antagonist bacteria and pathogen interaction significantly (p < 0.05) influenced the bacterial count, soil enzymes (chitinase and glucanase), and bacterial function (siderophore and chitinase production). These results indicated that these variables had an imperial role in disease suppression during plant development. Furthermore, the metabolic profiling showed that carbon source utilization enhanced under fruit development and ripening stages. These results suggested that carbon sources were essential in plant/pathogen/antagonist interaction. Substrates like β-methyl-D-glucoside, D-mannitol, D-galacturonic acid, N-acetyl-D-glucosamine, and phenylethylamine strongly connect with the suppuration of root rot disease. These carbon sources may help to propagate a healthy microbial community to reduce the pathogen invasion in the plant root system, and these carbon sources can be stimulators of antagonists against pathogens in the future.

Bio-organic soil amendment promotes the suppression of Ralstonia solanacearum by inducing changes in the functionality and composition of rhizosphere bacterial communities.

Stimulating the development of soil suppressiveness against certain pathogens represents a sustainable solution toward reducing pesticide use in agriculture. However, understanding the dynamics of suppressiveness and the mechanisms leading to pathogen control remain largely elusive. Here, we investigated the mechanisms used by the rhizosphere microbiome induces bacterial wilt disease suppression in a long-term field experiment where continuous application of bio-organic fertilizers (BFs) triggered disease suppressiveness when compared to chemical fertilizer application. We further demonstrated in a glasshouse experiment that the suppressiveness of the rhizosphere bacterial communities was triggered mainly by changes in community composition rather than only by the abundance of the introduced biocontrol strain. Metagenomics approaches revealed that members of the families Sphingomonadaceae and Xanthomonadaceae with the ability to produce secondary metabolites were enriched in the BF plant rhizosphere but only upon pathogen invasion. We experimentally validated this observation by inoculating bacterial isolates belonging to the families Sphingomonadaceae and Xanthomonadaceae into conducive soil, which led to a significant reduction in pathogen abundance and increase in nonribosomal peptide synthetase gene abundance. We conclude that priming of the soil microbiome with BF amendment fostered reactive bacterial communities in the rhizosphere of tomato plants in response to biotic disturbance.

Molecular characterization of endophytic and ectophytic plant growth promoting bacteria isolated from tomato plants (Solanum lycopersicum L.) grown in different soil types

BackgroundSuccessful rhizosphere colonization by plant growth promoting rhizobacteria (PGPR) is of crucial importance to perform the desired plant growth promoting activities. Since rhizocompetence is a dynamic process influenced by surrounding environmental conditions. In the present study, we hypothesized that bacterial isolates obtained from different tomato plant microhabitats (balk soil, rhizosphere, endorhiza, phyllosphere, and endoshoot) grown in different soils (sand, clay, and peat moss) will show different rhizocompetence abilities. ResultsTo evaluate this hypothesis, bacterial isolates were obtained from different plant microhabitats and screened for their phosphate solubilizing and nitrogen fixing activates. BOX-PCR fingerprint profiles showed high genotypic diversity among the tested isolates and that same genotypes were shared between different soils and/or plant microhabitats. 16S rRNA gene sequences of 25 PGP isolates, representing different plant spheres and soil types, were affiliated to eight genera: Enterobacter, Paraburkholderia, Klebsiella, Bacillus, Paenibacillus, Stenotrophomonas, Pseudomonas, and Kosakonia. The rhizocompetence of each isolate was evaluated in the rhizosphere of tomato plants grown on a mixture of the three soils. Different genotypes of the same bacterial species displayed different rhizocompetence potentials. However, isolates obtained from the above-ground parts of the plant showed high rhizocompetence. In addition, biological control-related genes, ituD and srfC, were detected in the obtained spore forming bacterial isolates. ConclusionThis study evaluates, for the first time, the relationship between plant microhabitat and the rhizocompetence ability in tomato rhizosphere. The results indicated that soil type and plant sphere can influence both the genotypic diversity and rhizocompetence ability of the same bacterial species. Bacterial isolates obtained in this study are promising to be used as an environmentally friendly substitution of chemical fertilizers.

Plant Growth-Promoting Activity of Pseudomonas aeruginosa FG106 and Its Ability to Act as a Biocontrol Agent against Potato, Tomato and Taro Pathogens.

Simple SummaryMicrobial bio-stimulants are attracting increasing attention in agricultural research. In particular, plant growth-promoting rhizobacteria (PGPR) have great potential to improve crops’ productivity and tolerance of biotic and abiotic stresses. It is anticipated that PGPR could eventually replace synthetic fungicides in agriculture. This research evaluated Pseudomonas aeruginosa strain FG106—which was isolated from tomato plants– as a potential biocontrol agent against several plant pathogens. This strain displayed multiple plant growth-promoting attributes and high in vitro and in vivo inhibition of growth and pathogenicity of tested phytopathogens. It is thus a multifunctional PGPR with potential applications as a biocontrol agent to control fungal and bacterial pathogens.P. aeruginosa strain FG106 was isolated from the rhizosphere of tomato plants and identified through morphological analysis, 16S rRNA gene sequencing, and whole-genome sequencing. In vitro and in vivo experiments demonstrated that this strain could control several pathogens on tomato, potato, taro, and strawberry. Volatile and non-volatile metabolites produced by the strain are known to adversely affect the tested pathogens. FG106 showed clear antagonism against Alternaria alternata, Botrytis cinerea, Clavibacter michiganensis subsp. michiganensis, Phytophthora colocasiae, P. infestans, Rhizoctonia solani, and Xanthomonas euvesicatoria pv. perforans. FG106 produced proteases and lipases while also inducing high phosphate solubilization, producing siderophores, ammonia, indole acetic acid (IAA), and hydrogen cyanide (HCN) and forming biofilms that promote plant growth and facilitate biocontrol. Genome mining approaches showed that this strain harbors genes related to biocontrol and growth promotion. These results suggest that this bacterial strain provides good protection against pathogens of several agriculturally important plants via direct and indirect modes of action and could thus be a valuable bio-control agent.

Genomic characterization and phytostimulative effect of a novel Serratia species

Some of non-pathogenic bacteria are effective biocontrol agents and plant growth inducers besides its degradative property on polycyclic aromatic hydrocarbons (PAH). Herein, we report a novel candidate Serratia species isolated in the purpose of PAH degradation, with its plant-growth-promoting and antifungal effect against Phytophthora infestans. Properties of bacterium determined by antifungal and phytostimulation assay under in vitro conditions displayed production of indole-3-acetic acid (IAA), chitinase and endoglucanase/cellulase activity. The identification of bacterium using whole-genome shotgun sequencing output also showed that the novel strain belongs to new Serratia species harboring the genes responsible for different secondary metabolites at the genomic level. Genome-wide analysis suggested a new candidate Serratia species (strain AGBY19) showing, in some extend, genetic relation with Serratia fonticola at molecular phylogeny level, which inhibits the growth of phytopathogenic fungi Phytophthora infestans by 73% compared to the control observed in vitro conditions. This strain colonised at the rhizosphere of tomato plant during in vivo host plant cultivation assay that remarkably enhanced the root growth. It causes the production of IAA hormone and cell wall degrading enzymes (chitinase, endoglucanase/cellulase). Further genome analyses of AGBY19 revealed different gene clusters comprising flanked regions associated with the production of secondary metabolites. These data eventually have provided its biocontrol properties and plant-growth inducer effect with globally potential to use for agricultural production.

Flavobacterium dauae sp. nov., isolated from rhizosphere soil of a tomato plant.

A bacterial strain, designated TCH3-2T, was isolated from the rhizosphere of tomato plant grown at Dong-A University Agricultural Experiment Station, Republic of Korea. The strain was Gram-stain-negative, obligate aerobic, orange yellow-coloured, motile by gliding and short rod-shaped. Strain TCH3-2 T only grew on 1/2 tryptic soy agar and Luria-Bertani agar among the media tested, with optimum growth at 28 °C and pH 7. Salt of 1 % NaCl was necessary to support the growth of TCH3-2T. Strain TCH3-2T produced flexirubin-type pigments. The predominant cellular fatty acids were iso-C15 : 0 (55.6 %), iso-C17 : 0 3-OH (17.9 %), summed feature 9 (comprising C16 : 0 10-methyl and/or iso-C17 : 1 ω9c; 10.5 %), iso-C15 : 0 3-OH (4.8 %) and anteiso-C15 : 0 (2.3 %). The major menaquinone was menaquinone-6 and the major polar lipids were phosphatidylethanolamine, five unknown aminolipids and three unknown lipids. Phylogenetic analysis based on 16S rRNA sequences indicated that TCH3-2T was closely related to Flavobacterium ummariense DS-12T (95.16 %), Flavobacterium marinum SW105T (95.14 %) and Flavobacterium viscosus YIM 102796T (94.54 %). The draft genome of TCH3-2T comprised ca. 2.8 Mb with a G+C content of 34.61 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between TCH3-2T and closely related Flavobacterium species showed that it belongs to a distinct species. Furthermore, the results of morphological, physiological and biochemical tests allowed further phenotypic differentiation of TCH3-2T from its closest relatives. Thus, chemotaxonomic characteristics together with phylogenetic affiliation illustrate that TCH3-2T represents a novel species of the genus Flavobacterium, for which the name Flavobacterium dauae sp. nov. (type strain TCH3-2T=KACC 19054T=JCM 34025T) is proposed.

Adding alfalfa to an annual crop rotation shifts the composition and functional responses of tomato rhizosphere microbial communities

Alfalfa (Medicago sativa L.) is widely cultivated to reduce nitrogen (N) fertilizer inputs for the subsequent crop and can improve soil nitrogen (N) availability and crop yields, widely referred to as the “rotation effect.” The soil mechanisms behind these effects may be due to changes associated with the rhizosphere microbial community of alfalfa. We hypothesized that a compositionally and functionally distinct microbial community would colonize the rhizosphere of tomato plants grown following alfalfa, compared to following maize, and that some of the microbial groups would be carried over from the alfalfa. We also hypothesized that including alfalfa in rotation would lead to greater abundance of genes associated with nitrogen cycling in the tomato rhizosphere. Amplicon sequencing targeting the 16s rDNA gene of bacteria and ITS of fungi were employed to characterize the functional and compositional diversity of the rhizosphere microbial community in two systems under tomato cultivation at the Russell Ranch Sustainable Agriculture Facility Century Experiment (Davis, CA, USA): i) maize-tomato rotation in which we sampled tomatoes (CMT); and ii) alfalfa-maize-tomato rotation in which we sampled tomatoes (AMTT) and alfalfa (AMTA). Bacterial and fungal communities were significantly different among the three systems, with AMTA showing the greatest differences from the others, consistent with the importance of plant species in recruiting specific rhizosphere microbial communities. Changes between the tomato systems were primarily due to increased abundances of bacterial groups Acidobacteria, Actinobacteria, Chloroflexi, Gemmatimonadetes and the fungal group Glomeromycota that includes arbuscular mycorrhizal fungi. The abundance of bacterial and fungal genera, Niastella, Kribbella and Preussia was similar in AMTA and AMTT but not in CMT, which suggests a carry-over effect from alfalfa to the subsequent tomato crop rhizosphere. Groups enriched or carried over into tomato included taxa with the ability to enhance soil nutrient availability, plant growth promotion, and suppress harmful effects of pathogens. Genes encoding enzymes related to denitrification were significantly less abundant in the tomato rhizosphere following alfalfa than maize. Improving our understanding of how crop rotation influences soil microbial community composition and functions could enable the designing of crop rotations to foster the proliferation of specific beneficial microbial groups.

A Gold Nanoparticle-Based Colorimetric Probe for Detection of Gibberellic Acid Exuded by Ralstonia solanacearum Pathogen in Tomato (Solanum lycopersicum L.)

We reported a simple colorimetric probe based on gold nanoparticles (AuNPs) for detecting Ralstonia solanacearum. The AuNPs were synthesized through reduction with citrate ion and characterized by ultraviolet-visible spectroscopy (UV-vis), scanning electron microscopy (SEM), and transmission electron microscopy (TEM). The freshly synthesized AuNPs were brick red due to an intense surface plasmon absorption band at 520 nm. Upon interaction with synthetic gibberellic acid (GA3), a bathochromic shift occurred in the surface plasmon resonance (SPR) peak of AuNPs to higher wavelengths. The 'eye-ball' limit of detection was 0.2 ppm. This shift was accompanied by a change in the color of the AuNPs from brick red to purple. Soil samples were collected from the rhizosphere of tomato plants, exhibiting bacterial wilt symptoms and pure cultures of Ralstonia solanacearum isolated using a modified Kelman’s TZC medium. Gibberellins (GA) were extracted from the culture of R. solanacearum using ethyl acetate and characterized using fourier transform infrared spectroscopy (FT-IR). AuNP solution aggregation was induced by GA-mediated R. solanacearum. A color change from brick red to purple was also observed. The results illustrated the use of both SPR wavelength-shift sensing and visual color change to detect molecules of biological relevance.

Paenibacillus lycopersici sp. nov. and Paenibacillus rhizovicinus sp. nov., isolated from the rhizosphere of tomato (Solanum lycopersicum).

Two Gram-stain-positive, rod-shaped, endospore-forming bacteria, designated 12200R-189T and 14171R-81T were isolated from the rhizosphere of tomato plants. The 16S rRNA gene sequence similarity between strains 12200R-189T and 14171R-81T were 97.2%. Both strains showed the highest 16S rRNA gene sequence similarities to Paenibacillus sacheonensis SY01T (96.3% and 98.0%, respectively). The genome of strain 12200R-189T was approximately 6.7 Mb in size with 5,750 protein-coding genes (CDSs) and the G + C content was 58.1 mol%, whereas that of strain 14171R-81T comprised one chromosome of 7.0 Mb and two plasmids (0.2 Mb each) with 6,595 CDSs and the G + C content was 54.5 mol%. Comparative genome analysis revealed that average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values among 12200R-189T, 14171R-81T, and other closely related species were below the cut-off levels 95% and 70%, respectively. Strain 12200R-189T grew at a temperature range of 15-40°C, pH 6.0-9.0, and 0-3% NaCl (w/v), whereas strain 14171R-81T grew at a temperature range of 10-37°C, pH 6.0-8.0, and 0-1% NaCl (w/v). Menaquinone-7 (MK-7) was the only isoprenoid quinone detected in both strains. The predominant cellular fatty acids (> 10%) were iso-C15:0, anteiso-C15:0, and iso-C16:0. The polar lipids of strain 12200R-189T were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), aminophospholipid (APL), phospholipid (PL), phosphatidylglycolipid (PGL), and four aminophosphoglycolipids (APGLs) and those of strain 14171R-81T were DPG, PG, PE, APL, three PLs, two PGLs, and three APGLs. Based on phylogenetic, genomic, phenotypic, and chemotaxonomic analyses, strains 12200R-189T and 14171R-81T represent two novel species of the genus Paenibacillus, for which the names Paenibacillus lycopersici sp. nov. and Paenibacillus rhizovicinus sp. nov. are proposed. The type strains are 12200R-189T (= KACC 19916T = CCTCC AB 2020027T) and 14171R-81T (= KACC 19915T = CCTCC AB 2020026T).

Effect of Physicochemical Parameters on Inorganic Phosphate Solubilisation by Serratia marcescens PH1 and Organic Acids Production

PHOSPHATE solubilizing bacteria are capable to release inorganic phosphate and make it available to plants for growth enhancement. In this study, Serratia marcescens PH1, which has been isolated from tomato plant rhizosphere, has been subjected to different physical and chemical parameters for optimization of its phosphate solubilisation capacity. The best temperature, inoculum percentage, agitation rate, incubation time, and pH value were found to be 30℃, 1.5%, 150rpm, 5 days, and 7-8, respectively. The best carbon source for phosphate solubilisation among 5 different sources, glucose, sucrose, galactose, maltose, and arabinose, was glucose which allows for releasing 797mg/L of P. Besides, casein was the best nitrogen source for phosphorus release (853mg/L) and Ca3(PO4)2 in Pikovskaya medium was the best P source (855mg/L). The key factors affecting P release in the modified Pikovskaya medium were glucose, casein and inoculum percentage. P concentration in the modified Pikovskaya culture medium was 853mg/ml comparing with only 749mg/L in the classical formula. For freeing of P, Serratia marcescens PH1 produces organic acids such as citric, lactic, malic, and benzoic acids. Phosphorus yield was increased gradually with organic acids production till reaching 861mg/ml in 5 days with pH drop to 1.1. pqqC (a gene responsible of PQQ production) gene fragment of approx. 568 bp was successfully amplified in phosphate solubilizing bacteria. Detection of pqq genes is an evidence of gluconic acid production capability. This acid is a well known biocontrol agent. Serratia marcescens PH1 is a strong phosphate solubilizer and we are planning to conduct more wide-scale experiments in pots to optimize the utilization of such bacterium before conducting agricultural applications as a plant growth promoter and a biocontrol agent.

Bacterial Tomato Pathogen Ralstonia solanacearum Invasion Modulates Rhizosphere Compounds and Facilitates the Cascade Effect of Fungal Pathogen Fusarium solani.

Soil-borne pathogen invasions can significantly change the microbial communities of the host rhizosphere. However, whether bacterial Ralstonia solanacearum pathogen invasion influences the abundance of fungal pathogens remains unclear. In this study, we combined high-throughput sequencing, qPCR, liquid chromatography and soil culture experiments to analyze the rhizosphere fungal composition, co-occurrence of fungal communities, copy numbers of functional genes, contents of phenolic acids and their associations in healthy and bacterial wilt-diseased tomato plants. We found that R. solanacearum invasion increased the abundance of the soil-borne pathogen Fusarium solani. The concentrations of three phenolic acids in the rhizosphere soil of bacterial wilt-diseased tomato plants were significantly higher than those in the rhizosphere soil of healthy tomato plants. In addition, the increased concentrations of phenolic acids significantly stimulated F. solani growth in the soil. Furthermore, a simple fungal network with fewer links, nodes and hubs (highly connected nodes) was found in the diseased tomato plant rhizosphere. These results indicate that once the symptom of bacterial wilt disease is observed in tomato, the roots of the wilt-diseased tomato plants need to be removed in a timely manner to prevent the enrichment of other fungal soil-borne pathogens. These findings provide some ecological clues for the mixed co-occurrence of bacterial wilt disease and other fungal soil-borne diseases.

A simple and stable method of tagging Agrobacterium fabrum C58 for environmental monitoring

Agrobacterium fabrum is one of the eleven Agrobacterium spp . complex species that has been observed to carry a Ti plasmid and induce crown gall, a disease causing significant damage to economically important perennial agricultural crops. Members of this species complex, including A. fabrum , are morphologically indistinguishable from one another on culture media and are known to grow together in soil and within host galls. Consequently, the tracking of this species in its natural environment requires a cautious approach to tagging strains without altering any of their ecologically important traits. A gentamicin resistant cassette ( aacC1 ) was inserted, by homologous recombination, into a non-coding region of the A. fabrum C58 chromosome between the genes atu1182 and atu1183 . The resultant strain did not show any significant in vitro growth differences compared to the wild-type strain, and the marker was stable in rich medium, both with and without selective pressure. The mutant/marked strain was indistinguishable from the parental strain for ability to induce galls, grow in bulk soil and colonize the rhizosphere of tomato plants. Easy, precise, safe and stable tagging of the A. fabrum C58 genome facilitates environmental population surveys by either simple selection or direct detection by PCR. This methodology provides understanding of the ecology of this species complex as an integral part of managing the soil microbiota for improved crown gall management.