Genomic and Phenotypic Insights Into the Potential of Rock Phosphate Solubilizing Bacteria to Promote Millet Growth in vivo

Improved efficiency of Sedum lineare (Crassulaceae) in remediation of arsenic-contaminated soil by phosphate-dissolving strain P-1 in association with phosphate rock

The selection of appropriate plants and growth strategies is a key factor in improving the efficiency and universal applicability of phytoremediation. Sedum lineare grows rapidly and tolerates multiple adversities. The effects of inoculation of Acinetobacter sp. phosphate solubilizing bacteria P-1 and application of phosphate rock (PR) as additives on the remediation efficiency of As-contaminated soil by S. lineare were investigated. Compared with the control, both the single treatment and the combination of inoculation with strain P-1 and application of PR improved the biomass by 30.7-395.5%, chlorophyll content by 48.1-134.8%, total protein content by 12.5-92.4% and total As accumulation by 45.1-177.5%, and reduced the As-induced oxidative damage. Inoculation with strain P-1 increased the activities of superoxide dismutases and catalases of S. lineare under As stress, decreased the accumulation of reactive oxygen species in plant tissues and promoted the accumulation of As in roots. In contrast, simultaneous application of PR decreased As concentration in S. lineare tissues, attenuated As-induced lipid peroxidation and improved As transport to shoots. In addition, the combined application showed the best performance in improving resistance and biomass, which significantly increased root length by 149.1%, shoot length by 33%, fresh weight by 395.5% and total arsenic accumulation by 159.2%, but decreased the malondialdehyde content by 89.1%. Our results indicate that the combined application of strain P-1 and PR with S. lineare is a promising bioremediation strategy to accelerate phytoremediation of As-contaminated soils.

Isolation and characterization of phosphate-solubilizing bacteria from rhizosphere of poplar on road verge and their antagonistic potential against various phytopathogens

BACKGROUND

Phosphate-solubilizing bacteria (PSB) can solubilize insoluble phosphate compounds and improve phosphate availability in soil. Road verges are important in urban landscaping, but the population structure of PSB and their ecological functions in the road verge soil is still unclear.

RESULTS

Twenty-one mineral PSB strains and 14 organic PSB strains were isolated from the rhizosphere of poplar on urban road verge. All the mineral PSB strains showed better solubilization to Ca3(PO4)2 than FePO4 or AlPO4. Among them, 7 strains showed high phosphate-solubilizing (PS) activities to Ca3(PO4)2 (150-453 mg/L). All the organic PSB strains displayed weak solubilization to lecithin. 16S rRNA gene-based phylogenetic analysis showed good species diversity of the PSB strains, which belongs to 12 genera: Bacillus, Cedecea, Cellulosimicrobium, Delftia, Ensifer, Paenibacillus, Pantoea, Phyllobacterium, Pseudomonas, Rhizobium, Sinorhizobium and Staphylococcus. Moreover, 8 PSB strains showed various degrees of growth inhibition against 4 plant pathogenic fungi, Fusarium oxysporum S1, F. oxysporum S2, Pythium deliense Meurs Z4, Phomopsis sp. AC1 and a plant pathogenic bacterium, Pectobacterium carotovorum TP1.

CONCLUSIONS

The results indicated that these PSB strains could perform multiple ecological functions on road verge. The development and application of bio-agents based on the strains would provide a new strategy for maintaining and improving the ecosystem stability of road verges.

Pathogen Profile of Klebsiella variicola, the Causative Agent of Banana Sheath Rot

Banana (Musa spp.) is an important fruit and food crop worldwide. In recent years, banana sheath rot has become a major problem in banana cultivation, causing plant death and substantial economic losses. Nevertheless, the pathogen profile of this disease has not been fully characterized. Klebsiella variicola is a versatile bacterium capable of colonizing different hosts, such as plants, humans, insects, and animals, and is recognized as an emerging pathogen in various hosts. In this study, we obtained 12 bacterial isolates from 12 different banana samples showing banana sheath rot in Guangdong and Guangxi Provinces, China. Phylogenetic analysis based on 16S rRNA sequences confirmed that all 12 isolates were K. variicola strains. We sequenced the genomes of these strains, performed comparative genomic analysis with other sequenced K. variicola strains, and found a lack of consistency in accessory gene content among these K. variicola strains. However, prediction based on the pan-genome of K. variicola revealed 22 unique virulence factors carried by the 12 pathogenic K. variicola isolates. Microbiome and microbial interaction network analysis of endophytes between the healthy tissues of diseased plants and healthy plants of two cultivars showed that Methanobacterium negatively interacts with Klebsiella in banana plants and that Herbaspirillum might indirectly inhibit Methanobacterium to promote Klebsiella growth. These results suggest that banana sheath rot is caused by the imbalance of plant endophytes and opportunistic pathogenic bacteria, providing an important basis for research and control of this disease.[Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Phosphate Solubilization and Plant Growth Promotion by Pantoea brenneri Soil Isolates

Phosphate solubilizing microorganisms (PSMs) in soil have been shown to reduce mineral phosphate fertilizer supplementation and promote plant growth. Nevertheless, only several P-solubilizing microorganisms capable of solubilizing both organic and mineral sources of soil phosphorus have been identified up to now. The aim of this study was to evaluate the inorganic soil phosphate solubilizing activity of phytate-hydrolyzing Pantoea brenneri soil isolates. We showed that the strains efficiently solubilize a variety of inorganic phosphates. We optimized the media composition and culturing conditions to improve the solubilization efficiency of the strains and investigated the mechanisms of their phosphate solubilization. Through HPLC analysis, it was determined that P. brenneri produce oxalic, malic, formic, malonic, lactic, maleic, acetic, and citric acids as well as acid and alkaline phosphatases while growing on insoluble phosphate sources. Finally, we analyzed the influence of P. brenneri strains with multiple PGP-treats on plant growth in greenhouse experiments and showed their ability to promote growth of potato.

Plant Growth-Promoting Rhizobacteria for Sustainable Agricultural Production

Rhizosheric bacteria with several abilities related to plant growth and health have been denominated Plant Growth-Promoting Rhizobacteria (PGPR). PGPR promote plant growth through several modes of action, be it directly or indirectly. The benefits provided by these bacteria can include increased nutrient availability, phytohormone production, shoot and root development, protection against several phytopathogens, and reduced diseases. Additionally, PGPR can help plants to withstand abiotic stresses such as salinity and drought and produce enzymes that detoxify plants from heavy metals. PGPR have become an important strategy in sustainable agriculture due to the possibility of reducing synthetic fertilizers and pesticides, promoting plant growth and health, and enhancing soil quality. There are many studies related to PGPR in the literature. However, this review highlights the studies that used PGPR for sustainable production in a practical way, making it possible to reduce the use of fertilizers such as phosphorus and nitrogen and fungicides, and to improve nutrient uptake. This review addresses topics such as unconventional fertilizers, seed microbiome for rhizospheric colonization, rhizospheric microorganisms, nitrogen fixation for reducing chemical fertilizers, phosphorus solubilizing and mineralizing, and siderophore and phytohormone production for reducing the use of fungicides and pesticides for sustainable agriculture.

Transcriptome profiling of genes regulated by phosphate-solubilizing bacteria Bacillus megaterium P68 in potato (Solanum tuberosum L.)

The insoluble phosphorus in the soil is extremely difficult to be absorbed and used directly through the potato root system. Although many studies have reported that phosphorus-solubilizing bacteria (PSB) can promote plant growth and uptake of phosphorus, the molecular mechanism of phosphorus uptake and growth by PSB has not been investigated yet. In the present study, PSB were isolated from rhizosphere soil in soybean. The data of potato yield and quality revealed that the strain P68 was the most effective In the present study, PSB identification, potato field experiment, pot experiment and transcriptome profiling to explored the role of PSB on potato growth and related molecular mechanisms. The results showed that the P68 strain (P68) was identified as Bacillus megaterium by sequencing, with a P-solubilizing ability of 461.86 mg·L^-1 after 7-day incubation in National Botanical Research Institute's Phosphate (NBRIP) medium. Compared with the control group (CK), P68 significantly increased the yield of potato commercial tubers by 17.02% and P accumulation by 27.31% in the field. Similarly, pot trials showed that the application of P68 significantly increased the biomass, total phosphorus content of the potato plants, and available phosphorus of the soil up by 32.33, 37.50, and 29.15%, respectively. Furthermore, the transcriptome profiling results of the pot potato roots revealed that the total number of bases was about 6G, and Q30 (%) was 92.35-94.8%. Compared with the CK, there were a total of 784 differential genes (DEGs) regulated when treated with P68, which 439 genes were upregulated and 345 genes were downregulated. Interestingly, most of the DEGs were mainly related to cellular carbohydrate metabolic process, photosynthesis, and cellular carbohydrate biosynthesis process. According to the KEGG pathway analysis, a total of 46 categorical metabolic pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database were annotated to 101 DEGs found in potato roots. Compared with the CK, most of the DEGs were mainly enriched in glyoxylate and dicarboxylate metabolism (sot00630), nitrogen metabolism (sot00910), tryptophan metabolism (sot00380), and plant hormone signal transduction (sot04075), and these DEGs might be involved in the interactions between Bacillus megaterium P68 and potato growth. The qRT-PCR analysis of differentially expressed genes showed that inoculated treatments P68 significantly upregulated expression of the phosphate transport, nitrate transport, glutamine synthesis, and abscisic acid regulatory pathways, respectively, and the data from qRT-PCR were consistent with that obtained from RNA-seq. In summary, PSB may be involved in the regulation of nitrogen and phosphorus nutrition, glutaminase synthesis, and abscisic acid-related metabolic pathways. This research would provide a new perspective for studying the molecular mechanism of potato growth promotion by PSB in the level of gene expression and related metabolic pathways in potato roots under the application of Bacillus megaterium P68.

Innovative Rhizosphere-Based Enrichment under P-Limitation Selects for Bacterial Isolates with High-Performance P-Solubilizing Traits

The use of phosphate solubilizing bacteria (PSB) as inoculants for the rhizosphere is a well-known strategy to mitigate P-deficiency in plants. However, despite the multiple modes of action to render P available for plants, PSB often fail to deliver in the field as their selection is often based on a single P-solubilizing trait assessed in vitro. Anticipating these shortcomings, we screened 250 isolates originating from rhizosphere-based enriched consortia for the main in vitro P-solubilizing traits, and subsequently grouped the isolates through trait-based HCPC (hierarchical clustering on principal components). Representative isolates of each cluster were tested in an in planta experiment to compare their in vitro P-solubilizing traits with their in planta performance under conditions of P-deprivation. Our data convincingly show that bacterial consortia capable to mitigate P-deficiency in planta were enriched in bacterial isolates that had multiple P-solubilizing traits in vitro and that had the capacity to mitigate plant P-stress in planta under P-deprived conditions. Furthermore, although it was assumed that bacteria that looked promising in vitro would also have a positive effect in planta, our data show that this was not always the case. Opposite, lack of performance in vitro did not automatically result in a lack of performance in planta. These results corroborate the strength of the previously described in planta-based enrichment and selection technique for the isolation of highly efficient rhizosphere competent PSB. IMPORTANCE With the growing awareness on the ecological impact of chemical phosphate fertilizers, research concerning the use of phosphate solubilizing bacteria (PSB) as a sustainable alternative for, or addition to these fertilizers is of paramount importance. In previous research, we successfully implemented a plant-based enrichment technique for PSB, which simultaneously selected for the rhizosphere competence and phosphate solubilizing characteristics of bacterial suspensions. Current research follows up on our previous findings, whereas we screened 250 rhizobacteria for their P-solubilizing traits and were able to substantiate the results obtained from the enriched suspensions at a single-isolate level. With this research, we aim for a paradigm shift toward the plant-based selection of PSB, which is a more holistic approach compared to the plate-based methods. We emphasize the strength of the previously described plant-based enrichment and selection technique for the isolation of highly efficient and diverse PSB.

Micropropagation of Seed-Derived Clonal Lines of the Endangered Agave marmorata Roezl and Their Compatibility with Endophytes

Simple Summary

The wild Agave marmorata Roezl has been classified as an endangered species. Extracting these plants from the forest for commercial purposes and long maturation periods of close to 30 years have contributed to their loss. A. marmorata interacts with pollinators and other Agaves species to maintain genetic variability. Thus, the conservation and restoration of the agave ecosystem is an ecological challenge. Typically, agave micropropagation use meristem or leaves as explants to rapidly produce uniform agave plants in age and size on a large scale leading to homogeneous plantations. However, introducing these clones to the field reduces genetic variability. This study evaluated in vitro micropropagation of A. marmorata from seeds to generate clonal lines. The selected seedlings exhibited variations in multiplication capacity and stable tissue formation. Variations in clonal lines could be exploited to produce high-quality plants with different capacities, such as faster propagation, enhanced stress adaptation, and continued growth under nutrient limitation conditions, consequently maintaining genetic variability. Furthermore, some clonal lines were inoculated with four endophytic bacteria to identify other differences among these plants, including endophyte-host compatibility. Variable responses to inoculation were observed among clonal lines. We found that Achromobacter xylosoxidans was compatible, unlike Enterobacter cloacae which caused plant death.

Abstract

A. marmorata is the raw material used for tepextate mescal production but is classified as an endangered species. In the present study, we obtain and multiply clonal lines of Agave marmorata Roezl by selecting seedlings derived from seeds. Ten seedlings from two lots of 400 germinated seeds were selected for axillary bud proliferation induced by BAP 5 mg/L in vitamin-free Murashige and Skoog’s medium. Differences in shoot numbers, heights and senescent tissue formation were observed. Notably, the AM32 line formed 84 shoots and presented low senescent tissue after 60 d of culture. We also selected the AM31 and AM33 clonal lines. Four-month shoots were extracted with 80% methanol in water to determine the total content of saponins, flavonoids, and phenolic acids and compare the three clonal lines. Some bioactive molecules were identified using HPLC techniques and MALDI-TOF mass spectrometry none showed significant differences in content. Additionally, plants derived from the clonal lines were inoculated with four endophytic bacteria. Among these, Achromobacter xylosoxidans supported plant growth of AM32. A notable effect of plant death was observed after inoculation with Enterobacter cloacae, an endophyte of A. tequilana. Additionally, Pseudomonas aeruginosa, an endophyte from A. marmorata, reduced biomass. Our results demonstrate the incompatibility of A. marmorata to E. cloacae and specialization between the host plant and its endophytes. The compatibility of the plant-endophyte could be exploited to boost the establishment and stability of mutualisms to benefit plant development, stress tolerance and pathogen resistance. The differences in multiplication capacity, stable tissue formation, and endophyte biotization responses may indicate genetic variability. Clonal selection and micropropagation from seed-derived plants could contribute to conserving the endangered A. marmorata plant for reforestation in their natural habitats, thus, assuring mass propagation for sustainable industrial production of mescal, bioactive compounds, and prebiotics.

Insight into soil nitrogen and phosphorus availability and agricultural sustainability by plant growth-promoting rhizobacteria

Nitrogen and phosphorus are critical for the vegetation ecosystem and two of the most insufficient nutrients in the soil. In agriculture practice, many chemical fertilizers are being applied to soil to improve soil nutrients and yield. This farming procedure poses considerable environmental risks which affect agricultural sustainability. As robust soil microorganisms, plant growth-promoting rhizobacteria (PGPR) have emerged as an environmentally friendly way of maintaining and improving the soil's available nitrogen and phosphorus. As a special PGPR, rhizospheric diazotrophs can fix nitrogen in the rhizosphere and promote plant growth. However, the mechanisms and influences of rhizospheric nitrogen fixation (NF) are not well researched as symbiotic NF lacks summarizing. Phosphate-solubilizing bacteria (PSB) are important members of PGPR. They can dissolve both insoluble mineral and organic phosphate in soil and enhance the phosphorus uptake of plants. The application of PSB can significantly increase plant biomass and yield. Co-inoculating PSB with other PGPR shows better performance in plant growth promotion, and the mechanisms are more complicated. Here, we provide a comprehensive review of rhizospheric NF and phosphate solubilization by PGPR. Deeper genetic insights would provide a better understanding of the NF mechanisms of PGPR, and co-inoculation with rhizospheric diazotrophs and PSB strains would be a strategy in enhancing the sustainability of soil nutrients.

Comparative Genome Analysis Reveals Phylogenetic Identity of Bacillus velezensis HNA3 and Genomic Insights into Its Plant Growth Promotion and Biocontrol Effects

Bacillus velezensis HNA3, a potential plant growth promoter and biocontrol rhizobacterium, was isolated from plant rhizosphere soils in our previous work. Here, we sequenced the entire genome of the HNA3 strain and performed a comparative genome analysis. We found that HNA3 has a 3,929-kb chromosome with 46.5% GC content and 4,080 CDSs. We reclassified HNA3 as a Bacillus velezensis strain by core genome analysis between HNA3 and 74 previously defined Bacillus strains in the evolutionary tree. A comparative genomic analysis among Bacillus velezensis HNA3, Bacillus velezensis FZB42, Bacillus amyloliquefaciens DSM7, and Bacillus subtilis 168 showed that only HNA3 has one predicated secretory protein feruloyl esterase that catalyzes the hydrolysis of plant cell wall polysaccharides. The analysis of gene clusters revealed that whole biosynthetic gene clusters type Lanthipeptide was exclusively identified in HNA3 and might lead to the synthesis of new bioactive compounds. Twelve gene clusters were detected in HNA3 responsible for the synthesis of 14 secondary metabolites including Bacillaene, Fengycin, Bacillomycin D, Surfactin, Plipastatin, Mycosubtilin, Paenilarvins, Macrolactin, Difficidin, Amylocyclicin, Bacilysin, Iturin, Bacillibactin, Paenibactin, and others. HNA3 has 77 genes encoding for possible antifungal and antibacterial secreting carbohydrate active enzymes. It also contains genes involved in plant growth promotion, such as 11 putative indole acetic acid (IAA)-producing genes, spermidine and polyamine synthase genes, volatile compound producing genes, and multiple biofilm related genes. HNA3 also has 19 phosphatase genes involved in phosphorus solubilization. Our results provide insights into the genetic characteristics responsible for the bioactivities and potential application of HNA3 as plant growth-promoting strain in ecological agriculture.

IMPORTANCE This study is the primary initiative to identify Bacillus velezensis HNA3 whole genome sequence and reveal its genomic properties as an effective biocontrol agent against plant pathogens and a plant growth stimulator. HNA3 genetic profile can be used as a reference for future studies that can be applied as a highly effective biofertilizer and biofungicide inoculum to improve agriculture productivity. HNA3 reclassified in the phylogenetic tree which may be helpful for highly effective strain engineering and taxonomy. The genetic comparison among HNA3 and closely similar species B. velezensis FZB42, B. amyloliquefaciens DSM7, and B. subtilis 168 demonstrates some distinctive genetic properties of HNA3 and provides a basis for the genetic diversity of the Bacillus genus, which allows developing more effective eco-friendly resources for agriculture and separation of Bacillus velezensis as distinct species in the phylogenetic tree.

Serratia plymuthica MBSA-MJ1 Increases Shoot Growth and Tissue Nutrient Concentration in Containerized Ornamentals Grown Under Low-Nutrient Conditions

High fertilizer rates are often applied to horticulture crop production systems to produce high quality crops with minimal time in production. Much of the nutrients applied in fertilizers are not taken up by the plant and are leached out of the containers during regular irrigation. The application of plant growth promoting rhizobacteria (PGPR) can increase the availability and uptake of essential nutrients by plants, thereby reducing nutrient leaching and environmental contamination. Identification of PGPR can contribute to the formulation of biostimulant products for use in commercial greenhouse production. Here, we have identified Serratia plymuthica MBSA-MJ1 as a PGPR that can promote the growth of containerized horticulture crops grown with low fertilizer inputs. MBSA-MJ1 was applied weekly as a media drench to Petunia×hybrida (petunia), Impatiens walleriana (impatiens), and Viola×wittrockiana (pansy). Plant growth, quality, and tissue nutrient concentration were evaluated 8weeks after transplant. Application of MBSA-MJ1 increased the shoot biomass of all three species and increased the flower number of impatiens. Bacteria application also increased the concentration of certain essential nutrients in the shoots of different plant species. In vitro and genomic characterization identified multiple putative mechanisms that are likely contributing to the strain’s ability to increase the availability and uptake of these nutrients by plants. This work provides insight into the interconnectedness of beneficial PGPR mechanisms and how these bacteria can be utilized as potential biostimulants for sustainable crop production with reduced chemical fertilizer inputs.