Promotion of iron nutrition and growth on peanut by Paenibacillus illinoisensis and Bacillus sp. strains in calcareous soil

The potential of arbuscular mycorrhizal fungi to enhance metallic micronutrient uptake and mitigate food contamination in agriculture: prospects and challenges

Optimizing agroecosystems and crops for micronutrient uptake while reducing issues with inorganic contaminants (metal(loid)s) is a challenging task. One promising approach is to use arbuscular mycorrhizal fungi (AMF) and investigate the physiological, molecular and epigenetic changes that occur in their presence and that lead to changes in plant metal(loid) concentration (biofortification of micronutrients or mitigation of contaminants). Moreover, it is important to understand these mechanisms in the context of the soil microbiome, particularly those interactions of AMF with other soil microbes that can further shape crop nutrition. To address these challenges, a two-pronged approach is recommended: exploring molecular mechanisms and investigating microbiome management and engineering. Combining both approaches can lead to benefits in human health by balancing nutrition and contamination caused by metal(loid)s in the agro-ecosystem.

Unveiling growth-promoting attributes of peanut root endophyte Micromonospora sp

In this study, 20 endophytic actinobacteria were isolated from different parts of peanut plants growing in cropland with low and high salt in West Bengal, India. The endophytes underwent a rigorous morphological, biochemical, and genetic screening process to evaluate their effectiveness in enhancing plant growth. About 20% of these isolates were identified as potential plant growth-promoting endophytic actinobacteria, which showed high 16S rRNA gene sequence similarity (up to 99-100%) with different species of Micromonospora. Among these isolates, Micromonospora sp. ASENR15 produced the highest levels of indole acetic acid (IAA) and gibberellic acid (GA), while Micromonospora sp. ASENL2, Micromonospora sp. ANENR4, and Micromonospora sp. ASENR12 produced the highest level of siderophore. Among these leaf and root endophytic Micromonospora, strain ANENR4 was tested for its plant growth-promoting attributes. ANENR4 can be transmitted into the roots of a healthy peanut plant, enhances growth, and colonize the roots in abundance, suggesting the potential agricultural significance of the strain. Moreover, the study is the first report of endophytic Micromonospora in peanuts with PGP effects. The outcomes of this study open avenues for further research on harnessing the benefits of this endophytic Micromonospora for optimizing plant growth in agriculture.

Impact of soybean-associated plant growth-promoting bacteria on plant growth modulation under alkaline soil conditions

Conventional strategies to manage iron (Fe) deficiency still present drawbacks, and more eco-sustainable solutions are needed. Knowledge on soybean-specific diversity and functional traits of their plant growth-promoting bacteria (PGPB) potentiates their applicability as bioinoculants to foster soybean performance under calcareous soil conditions. This work aimed to assess the efficacy of PGPB, retrieved from soybean tissues/rhizosphere, in enhancing plant growth and development as well as crop yield under alkaline soil conditions. Seventy-six bacterial strains were isolated from shoots (18%), roots (53%), and rhizosphere (29%) of soybean. Twenty-nine genera were identified, with Bacillus and Microbacterium being the most predominant. Based on distinct plant growth-promoting traits, the endophyte Bacillus licheniformis P2.3 and the rhizobacteria Bacillus aerius S2.14 were selected as bioinoculants. In vivo tests showed that soybean photosynthetic parameters, chlorophyll content, total fresh weight, and Fe concentrations were not significantly affected by bioinoculation. However, inoculation with B. licheniformis P2.3 increased pod number (33%) and the expression of Fe-related genes (FRO2, IRT1, F6'H1, bHLH38, and FER4), and decreased FC-R activity (45%). Moreover, bioinoculation significantly affected Mn, Zn, and Ca accumulation in plant tissues. Soybean harbors several bacterial strains in their tissues and in the rhizosphere with capacities related to Fe nutrition and plant growth promotion. The strain B. licheniformis P2.3 showed the best potential to be incorporated in bioinoculant formulations for enhancing soybean performance under alkaline soil conditions.

Dual inoculation with rhizosphere-promoting bacterium Bacillus cereus and beneficial fungus Peniophora cinerea improves salt stress tolerance and productivity in willow

Utilization of rhizosphere microorganisms to improve plant growth and salt tolerance has recently attracted widespread attention. The growth and salt tolerance of willows inoculated with Bacillus cereus JYZ-SD2 and Peniophora cinerea XC were studied under different salt stress conditions. The results showed that the chlorophyll content of willow cuttings inoculated with the XC strain increased significantly by 51.27%. After salt stress of willow cuttings inoculated with B. cereus JYZ-SD2 and P. cinerea XC (solely or in combination), the amount of sodium in the roots from the epidermis to the pericycle decreased and the content of sodium in the pericycle was significantly lower than that of the uninoculated willow, while the proportion of potassium increased. Willow cuttings inoculated with microorganisms showed increased activity of SOD and POD. At the salt concentration of 100 mmol/L, the highest SOD activity was found in B. cereus JYZ-SD2-inoculated willows, with 59.88% increase compared to uninoculated willows; the highest POD activity was found in P. cinerea XC and B. cereus JYZ-SD2 co-inoculated willows, with 51.05% increase compared to uninoculated willows. The Na-K-ATPase and Ca-Mg-ATPase activities of inoculated P. cinerea XC willow cuttings were also 59.38% and 60% higher than that of uninoculated willows, respectively. The qPCR analysis showed that the expression of vp2 gene in the microorganism-inoculated willow leaves was always higher than that in willow alone. The expression of vp2 gene in P. cinerea XC-inoculated willow cuttings was 270.81% higher than that in uninoculated willows. Further observation of the ultrastructure of root cells under salt stress revealed that most of the vesicles in the root tip cells of willow were intact and secreted phagocytic vesicles to absorb sodium ions in the cytoplasm. This study shows that the combined beneficial fungi and rhizosphere-promoting bacteria inoculation technology as a practical biotechnological approach to enhance the growth of willows in salt-affected soils.

Bacterial Siderophores: Classification, Biosynthesis, Perspectives of Use in Agriculture

Siderophores are synthesized and secreted by many bacteria, yeasts, fungi, and plants for Fe (III) chelation. A variety of plant-growth-promoting bacteria (PGPB) colonize the rhizosphere and contribute to iron assimilation by plants. These microorganisms possess mechanisms to produce Fe ions under iron-deficient conditions. Under appropriate conditions, they synthesize and release siderophores, thereby increasing and regulating iron bioavailability. This review focuses on various bacterial strains that positively affect plant growth and development through synthesizing siderophores. Here we discuss the diverse chemical nature of siderophores produced by plant root bacteria; the life cycle of siderophores, from their biosynthesis to the Fe-siderophore complex degradation; three mechanisms of siderophore biosynthesis in bacteria; the methods for analyzing siderophores and the siderophore-producing activity of bacteria and the methods for screening the siderophore-producing activity of bacterial colonies. Further analysis of biochemical, molecular-biological, and physiological features of siderophore synthesis by bacteria and their use by plants will allow one to create effective microbiological preparations for improving soil fertility and increasing plant biomass, which is highly relevant for sustainable agriculture.

Rahnella aquatilis JZ-GX1 alleviates iron deficiency chlorosis in Cinnamomum camphora by secreting desferrioxamine and reshaping the soil fungal community

Plant growth-promoting rhizobacteria are important for improving plant iron nutrition, but the interactions among inoculants, host plants and soil microorganisms have not been greatly explored. Rahnella aquatilis JZ-GX1 was applied to treat the increasingly serious iron deficiency chlorosis in Cinnamomum camphora, and the resulting improvement in chlorosis was determined by assessing the contents of chlorophyll, active iron, Fe²⁺ and antioxidant enzymes in leaves, the effects on the soil microbial community and the metabolism in the rhizosphere by high-throughput sequencing techniques and liquid chromatography-mass spectrometry (LC-MS). The results showed that inoculation with JZ-GX1 significantly increased the chlorophyll content of C. camphora, which promoted the redistribution of active iron in roots and leaves, increased the activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) and ascorbate peroxidase (APX), and thus reduced membrane damage in iron-deficient C. camphora caused by reactive oxygen species. According to genome prediction and ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) analysis, the JZ-GX1 strain could secrete desferrioxamine (DFO), and the concentration of DFO in C. camphora rhizosphere was 21-fold higher than that in uninoculated soil. The exogenous application of DFO increased the SPAD and Fe²⁺ contents in leaves. In addition, the inoculant affected the fungal community structure and composition in the C. camphora rhizosphere soil and increased the abundances of specific taxa, such as Glomus, Mortierella, Trichoderma, and Penicillium. Therefore, R. aquatilis JZ-GX1 application promoted iron absorption in C. camphora trees by secreting DFO and alleviated iron deficiency chlorosis through interactions with the local fungal community.

Physiological and Transcriptome Analyses Revealed the Mechanism by Which Deferoxamine Promotes Iron Absorption in Cinnamomum camphora

Iron deficiency causes chlorosis and growth inhibition in Cinnamomum camphora, an important landscaping tree species. Siderophores produced by plant growth-promoting rhizobacteria have been widely reported to play an indispensable role in plant iron nutrition. However, little to date has been determined about how microbial siderophores promote plant iron absorption. In this study, multidisciplinary approaches, including physiological, biochemical and transcriptome methods, were used to investigate the role of deferoxamine (DFO) in regulating Fe availability in C. camphora seedlings. Our results showed that DFO supplementation significantly increased the Fe²⁺ content, SPAD value and ferric-chelate reductase (FCR) activity in plants, suggesting its beneficial effect under Fe deficiency. This DFO-driven amelioration of Fe deficiency was further supported by the improvement of photosynthesis. Intriguingly, DFO treatment activated the metabolic pathway of glutathione (GSH) synthesis, and exogenous spraying reduced glutathione and also alleviated chlorosis in C. camphora. In addition, the expression of some Fe acquisition and transport-related genes, including CcbHLH, CcFRO6, CcIRT2, CcNramp5, CcOPT3 and CcVIT4, was significantly upregulated by DFO treatment. Collectively, our data demonstrated an effective, economical and feasible organic iron-complexing agent for iron-deficient camphor trees and provided new insights into the mechanism by which siderophores promote iron absorption in plants.

Application of microbe-impregnated tannery solid waste biochar in soil enhances growth performance of sunflower

Synergistic effect of biochar and microbes in soil enhances performance of plants. Hazardous tannery solid waste can be reduced by one-third in volume by conversion to biochar. A greenhouse trial was set up with soil having different doses of metal resistant microbe-impregnated biochar (MIBC) prepared from tannery solid waste. Consortia of autochthonous strains of Trichoderma and Bacillus were inoculated on BC and the behavior and fate of metals were evaluated for their bioavailability to sunflower. Sunflower was grown in pots for 80 days having six different amendments of tannery solid waste biochar (0-10% w/w) with and without Trichoderma and Bacillus consortia and its morphological and biochemical attributes as well as metal uptake were observed. The results illustrated that application of BC at 2% rate without inoculation increased the shoot length and dry biomass by 19.8% and 77.4%, respectively, while plant growth and performance were reduced at higher amendments of BC. However, application of MIBC with Trichoderma or/and Bacillus consortium significantly improved the plant attributes at all levels of amendment. The results indicated that MIBC having Trichoderma and Bacillus consortia at 10% rate increased shoot length and dry biomass by 65.3% and 516% compared to control without BC. Application of BC without inoculation reduced the uptake of Cu, Fe, and Ni and increased the mobilization of all other metals for uptake in sunflower. Mobilization and uptake of Cd, Cr, Cu, Ni, Pb, and Zn decreased with MIBC having Trichoderma and Bacillus consortia whereas that of Fe and Mg were noted. A considerable decrease in proline and total phenolic content was demonstrated by MIBC-grown sunflower. The data of metal fractionation in BC also supported the above findings. Therefore, MIBC can be used as a promising option for enhancing growth performance and ensuring the physiological safety of sunflower as an energy crop.

The Genome of Bacillus velezensis SC60 Provides Evidence for Its Plant Probiotic Effects

Root colonization and plant probiotic function are important traits of plant growth-promoting rhizobacteria (PGPR). Bacillus velezensis SC60, a plant endophytic strain screened from Sesbania cannabina, has a strong colonization ability on various plant roots, which indicates that SC60 has a preferable adaptability to plants. However, the probiotic function of the strain SC60 is not well-understood. Promoting plant growth and suppressing soil-borne pathogens are key to the plant probiotic functions. In this study, the genetic mechanism of plant growth-promoting and antibacterial activity of the strain SC60 was analyzed by biological and bioinformatics methods. The complete genome size of strain SC60 was 3,962,671 bp, with 4079 predicted genes and an average GC content of 46.46%. SC60 was designated as Bacillus velezensis according to the comparative analysis, including average nucleotide polymorphism (ANI), digital DNA–DNA hybridization (dDDH), and phylogenetic analysis. Genomic secondary metabolite analyses indicated two clusters encoding potential new antimicrobials. The antagonism experiments revealed that strain SC60 had the ability to inhibit the growth of a variety of plant pathogens and its closely related strains of Bacillus spp., which was crucial to the rhizospheric competitiveness and growth-promoting effect of the strain. The present results further suggest that B. velezensis SC60 could be used as a PGPR strain to develop new biocontrol agents or microbial fertilizers.

Radiochemical Evidence for the Contribution of Chemotyped Siderophore Producing Bacteria Towards Plant Iron Nutrition

Fe deficiency is a major challenge that limits agricultural productivity and is a serious human health concern worldwide. Under iron-limiting conditions soil microorganisms produce siderophores, that chelates Fe³⁺ (ferric) and make it available to the plants. Selection of efficient siderophore producing bacteria and establishing their role in enhancing iron uptake is a strategic approach for improving plant nutrition. Hence 3 efficient isolates Pantoea agglomerans, Pseudomonas plecoglossida and Lactococcus lactis, selected from a repository of 154 bacteria, producing catecholate, hydroxamate and carboxylate siderophores, respectively, were assessed for Fe chelation efficiency using ⁵⁹Fe and their role in plant biometric parameters, Fe uptake and antioxidant enzymes with tomato (Strategy I) and wheat (Strategy II) test plants under hydroponic system. Cell-free siderophore preparation (Sid) improved plant parameters and iron nutrition more efficiently than bacterial inoculants. Pantoea agglomerans was proven best as its ⁵⁹Fe-bound siderophore complex showed the highest uptake of 4.25 and 1.59 Bq plant^-1 in wheat and tomato, respectively. Further, the Fe-starved plants (1 µm Fe-EDTA) showed around two-fold higher ⁵⁹Fe uptake than those raised under Fe-sufficient condition (100 µm Fe-EDTA). Results indicated that probably the bacterial mediated iron translocation in plants is Strategy III, complementing both Strategy I and II by facilitating higher availability of chelated Fe to plant reductases directly and/or through ligand exchange with phytosiderophores, respectively. This study highlights the need for integration of siderophore based formulations in INM strategies for enhancing plant iron content to address the Fe deficiency challenge of the soil and human nutrition.

Impact of Plant-Associated Bacteria on the In Vitro Growth and Pathogenic Resistance against Phellinus tremulae of Different Aspen (Populus) Genotypes

Aspens (Populus tremula and its hybrids), economically and ecologically important fast-growing trees, are often damaged by Phellinus tremulae, a rot-causing fungus. Plant-associated bacteria can be used to increase plant growth and resistance; however, no systematic studies relating the activity of symbiotic bacteria to aspen resistance against Phellinus tremulae have been conducted so far. The present pioneer study investigated the responses of two Populus tremula and two P. tremula × P. tremuloides genotypes to in vitro inoculations with, first, either Pseudomonas sp. or Paenibacillus sp. bacteria (isolated originally from hybrid aspen tissue cultures and being most closely related to Pseudomonas oryzihabitans and Paenibacillus tundrae, respectively) and, in the subsequent stage, with Phellinus tremulae. Both morphological parameters of in vitro-grown plants and biochemical content of their leaves, including photosynthesis pigments and secondary metabolites, were analyzed. It was found that both Populus tremula × P. tremuloides genotypes, whose development in vitro was significantly damaged by Phellinus tremulae, were characterized by certain responses to the studied bacteria: decreased shoot development by both Paenibacillus sp. and Pseudomonas sp. and increased phenol content by Pseudomonas sp. In turn, these responses were lacking in both Populus tremula genotypes that showed in vitro resistance to the fungus. Moreover, these genotypes showed positive long-term growth responses to bacterial inoculation, even synergistic with the subsequent fungal inoculation. Hence, the studied bacteria were demonstrated as a potential tool for the improved in vitro propagation of fungus-resistant aspen genotypes.

Competition, Nodule Occupancy, and Persistence of Inoculant Strains: Key Factors in the Rhizobium-Legume Symbioses

Biological nitrogen fixation by Rhizobium-legume symbioses represents an environmentally friendly and inexpensive alternative to the use of chemical nitrogen fertilizers in legume crops. Rhizobial inoculants, applied frequently as biofertilizers, play an important role in sustainable agriculture. However, inoculants often fail to compete for nodule occupancy against native rhizobia with inferior nitrogen-fixing abilities, resulting in low yields. Strains with excellent performance under controlled conditions are typically selected as inoculants, but the rates of nodule occupancy compared to native strains are rarely investigated. Lack of persistence in the field after agricultural cycles, usually due to the transfer of symbiotic genes from the inoculant strain to naturalized populations, also limits the suitability of commercial inoculants. When rhizobial inoculants are based on native strains with a high nitrogen fixation ability, they often have superior performance in the field due to their genetic adaptations to the local environment. Therefore, knowledge from laboratory studies assessing competition and understanding how diverse strains of rhizobia behave, together with assays done under field conditions, may allow us to exploit the effectiveness of native populations selected as elite strains and to breed specific host cultivar-rhizobial strain combinations. Here, we review current knowledge at the molecular level on competition for nodulation and the advances in molecular tools for assessing competitiveness. We then describe ongoing approaches for inoculant development based on native strains and emphasize future perspectives and applications using a multidisciplinary approach to ensure optimal performance of both symbiotic partners.

Phytostimulation and biocontrol potential of Gram-positive endospore-forming Bacilli

The spore-forming Bacillus and Paenibacillus species represent the phyla of beneficial bacteria for application as agricultural inputs in form of effective phytostimulators, biofertilizers, and biocontrol agents. The members of the genera Bacillus and Paenibacillus isolated from several ecological habitats are been thoroughly dissected for their effective application in the development of sustainable and eco-friendly agriculture. Numerous Bacillus and Paenibacillus species are reported as plant growth-promoting bacteria influencing the health and productivity of the food crops. This review narrates the mechanisms utilized by these species to enhance bioavailability and/or facilitate the acquisition of nutrients by the host plant, modulate plant hormones, stimulate host defense and stress resistance mechanisms, exert antagonistic action against soil and airborne pathogens, and alleviate the plant health. The mechanisms employed by Bacillus and Paenibacillus are seldom mutually exclusive. The comprehensive and systematic exploration of the aforementioned mechanisms in conjunction with the field investigations may assist in the exploration and selection of an effective biofertilizer and a biocontrol agent. This review aims to gather and discuss the literature citing the applications of Bacillus and Paenibacillus in the management of sustainable agriculture.

Identification of Plant Growth Promoting Rhizobacteria That Improve the Performance of Greenhouse-Grown Petunias under Low Fertility Conditions

The production of greenhouse ornamentals relies on high fertilizer inputs to meet scheduling deadlines and quality standards, but overfertilization has negative environmental impacts. The goals of this study were to identify plant-growth-promoting rhizobacteria (PGPR) that can improve greenhouse ornamental crop performance with reduced fertilizer inputs, and to identify the best measurements of plant performance for assessing the beneficial impact of PGPR on ornamentals. A high-throughput greenhouse trial was used to identify 14 PGPR isolates that improved the flower/bud number and shoot dry weight of Petunia × hybrida ‘Picobella Blue’ grown under low fertility conditions in peat-based media. These 14 PGPR were then applied to petunias grown under low fertility conditions (25 mg L⁻¹ N). PGPR-treated plants were compared to negative (untreated at 25 mg L⁻¹ N) and positive (untreated at 50, 75, 100, and 150 mg L⁻¹ N) controls. Multiple parameters were measured in the categories of flowering, vegetative growth, and vegetative quality to determine the best measurements to assess improvements in ornamental plant performance. Caballeronia zhejiangensis C7B12-treated plants performed better in almost all parameters and were comparable to untreated plants fertilized with 50 mg L⁻¹ N. Genomic analysis identified genes that were potentially involved in plant growth promotion. Our study identified potential PGPR that can be used as biostimulants to produce high-quality greenhouse ornamentals with lower fertilizer inputs.

Proteomics-based identification of orchid-associated bacteria colonizing the Epipactis albensis, E. helleborine and E. purpurata (Orchidaceae, Neottieae)

Using proteomics-based identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), we conducted the first analysis of the composition of endophytic bacteria isolated from different parts of selected Epipactis species, i.e. the buds, the inflorescences and the central part of the shoots, as well as the rhizomes. We identified aerobic and anaerobic bacteria, including such taxa as Bacillus spp., Clostridium spp., Pseudomonas spp. and Stenotrophomonas spp., which may be considered as promoting plant growth. Because most of the indicated bacteria genera belong to spore-producing taxa (spores allow bacterial symbionts to survive adverse conditions), we suggest that these bacteria species contribute to the adaptation of orchids to the environment. We found clear differences in the microbiome between investigated closely related taxa, i.e., Epipactis albensis, E. helleborine, E. purpurata and E. purpurata f. chlorophylla. Some of the analysed orchid species, i.e. E. albensis and E. purpurata co-occur in habitats, and their bacterial microbiomes differ from each other.

Oak (Quercus robur) Associated Endophytic Paenibacillus sp. Promotes Poplar (Populus spp.) Root Growth In Vitro

Soil fertilization is necessary for high-demand crop production in agriculture and forestry. Our current dependence on chemical fertilizers has significant harmful side effects. Biofertilization using microorganisms is a sustainable way to limit the need for chemical fertilizers in various enterprises. Most plant endophytic bacteria have thus far been unstudied for their plant growth promoting potential and hence present a novel niche for new biofertilizer strains. We isolated English oak (Quercus robur) endophytic bacteria and tested them for plant growth promoting traits (PGPTs) such as nitrogen fixation, phosphate mineralization/solubilization, siderophore and indole-3-acetic acid (IAA) production. We also investigated the effect the selected isolate had on poplar (Populus spp.) microshoot vegetative growth parameters in vitro. In total 48 bacterial strains were isolated, attributed to Bacillus, Delftia, Paenibacillus, Pantoea and Pseudomonas genera. All the isolates displayed at least three PGPTs, with 39.6% of the isolates displaying all five (all were Pseudomonas spp.) and 18.75% displaying four. Based on relative abundance, Paenibacillus sp. isolate was selected for the poplar microshoot inoculation study. The isolate had a significant positive effect on poplar microshoot root growth and development. Two tested poplar genotypes both had increased lateral root number and density, fresh and dry root biomass. Furthermore, one genotype had increased length and number of adventitious roots as well as a decrease in fresh aboveground biomass. The root enhancement was attributed to IAA production. We propose this isolate for further studies as a potential biofertilizer.

Ecosystem Functions of Microbial Consortia in Sustainable Agriculture

Knowledge of the agricultural soil microbiota, of the microbial consortia that comprise it, and the promotion of agricultural practices that maintain and encourage them, is a promising way to improve soil quality for sustainable agriculture and to provide food security. Although numerous studies have demonstrated the positive effects of beneficial soil microorganisms on crop yields and quality, the use of microbial consortia in agriculture remains low. Microbial consortia have more properties than an individual microbial inoculum, due to the synergy of the microorganisms that populate them. This review describes the main characteristics, ecosystem functions, crop benefits, and biotechnological applications of microbial consortia composed of arbuscular mycorrhizal fungi (AMF), plant growth-promoting rhizobacteria (PGPR), and Actinobacteria, to promote the restoration of agricultural soils and, consequently, the quality and health of agricultural crops. The aim is to provide knowledge that will contribute to the development of sustainable and sufficiently productive agriculture, which will adapt in a good way to the pace of the growing human population and to climate change.

Genome-based reclassification of Paenibacillus panacisoli DSM 21345T as Paenibacillus massiliensis subsp. panacisoli subsp. nov. and description of Paenibacillus massiliensis subsp. massiliensis subsp. nov

Bacteria of the genus Paenibacillus are relevant to humans, animals and plants. The species Paenibacillus massiliensis and Paenibacillus panacisoli are Gram-stain-positive and endospore-forming bacilli isolated from a blood culture of a leukemia patient and from soil of a ginseng field, respectively. Comparative analyses of their 16S rRNA genes revealed that the two Paenibacillus species could be synonyms (99.3% sequence identity). In the present study we performed different genomic analyses in order to evaluate the phylogenetic relationship of these micro-organisms. Paenibacillus massiliensis DSM 16942T and P. panacisoli DSM 21345T presented a difference in their G+C content lower than 1 mol%, overall genome relatedness index values higher than the species circumscription thresholds (average nucleotide identity, 95.57 %; genome-wide ANI, =96.51 %; and orthologous ANI, 96.25 %), and a monophyletic grouping pattern in the phylogenies of the 16S rRNA gene and the proteome core. Considering that these strains present differential biochemical capabilities and that their computed digital DNA–DNA hybridization value is lower than the cut-off for bacterial subspecies circumscription, we suggest that each of them form different subspecies of P. massiliensis , Paenibacillus massiliensis subsp. panacisoli subsp. nov. (type strain DSM 21345T) and Paenibacillus massiliensis subsp. massiliensis subsp. nov. (type strain DSM 16942T).

Exploring the efficacy of antagonistic rhizobacteria as native biocontrol agents against tomato plant diseases

As the environmental and health concerns alert the necessity to move towards a sustainable agriculture system, biological approach using indigenous plant growth-promoting rhizobacteria (PGPR) gains a strong impetus in the field of plant disease control. In this context, the present review article addresses the usage of rhizospheric antagonistic bacteria as a suitable alternative to control tomato fungal diseases namely Fusarium wilt and early blight disease. Biological control has been considered to be an eco-friendly, safe and effective method for disease management. The inherent traits of PGPR to antagonize a pathogen through various mechanisms has been investigated extensively to utilize them as potent biocontrol agents (BCA). Hence, the article provides a detailed account on different biocontrol mechanisms displayed by BCA. It is also suggested that the use of bacterial consortium ensures consistent performance by BCA in field conditions. Likewise, this review also deals with the opportunities and obstacles faced during commercialization of these antagonistic bacteria as biocontrol agents in the market.

Amelioration of chromium and heat stresses in Sorghum bicolor by Cr6+ reducing-thermotolerant plant growth promoting bacteria

Climatic factors particularly increased atmospheric temperature (IAT) greatly alters plant microbe and heavy metal interactions and subsequently reduces plant growth and phytoremediation efficiency. The aim of the study was to assess the effects of inoculation of chromium reducing-thermotolerant plant growth promoting bacteria (CRT-PGPB) on plant growth, physiological responses and chromium (Cr) uptake by Sorghum bicolor under IAT condition. Three potential CRT-PGPB strains were isolated from Cr contaminated sites and identified as Bacillus cereus TCR17, Providencia rettgeri TCR21 and Myroides odoratimimus TCR22 through molecular characterization. These strains displayed the potential to reduce Cr⁶⁺ to Cr³⁺, produce siderophores, indole-3-acetic acid and solubilize phosphate. Inoculation of S. bicolor with CRT-PGPB increased plant growth, antioxidant status (superoxide dismutase, catalase and ascorbate peroxidase) and decreased proline and malondialdehyde contents in plants under Cr, IAT and Cr + IAT stress indicate that PGPB helped plants to reduce stress induced oxidative damage. Irrespective of IAT stress, inoculation of CRT-PGPB decreased the accumulation of Cr in plants compared with un-inoculated control suggest that CRT-PGPB might have the potential to improve phytostabilization process in Cr contaminated soils. Furthermore, gene expression studies confirmed that inoculation of TCR21 down-regulated the expression of proline synthesis gene (p5cs1) and up-regulated the expression of antioxidant related genes (sod, apx1 and cat) and stress tolerance genes (sHsp). Our results showed that CRT-PGPB exhibiting potential to tolerate Cr, temperature, produce plant beneficial metabolites and reduce Cr⁶⁺ to Cr³⁺, can be exploited as potential inoculants for improving plant growth and phytoremediation process in Cr contaminated soil under IAT condition.

Systematic review of descriptions of novel bacterial species: evaluation of the twenty-first century taxonomy through text mining

Although described bacterial species increased in the twenty-first century, they correspond to a tiny fraction of the actual number of species living on our planet. The volume of textual data of these descriptions constitutes valuable information for revealing trends that in turn could support strategies for improvement of bacterial taxonomy. In this study, a text mining approach was used to generate bibliometric data to verify the state-of-art of bacterial taxonomy. Around 9700 abstracts of bacterial classification containing the expression 'sp. nov.' and published between 2001 and 2018 were downloaded from PubMed and analysed. Most articles were from PR China and the Republic of Korea, and published in the International Journal of Systematic and Evolutionary Microbiology. From about 10 800 species names detected, 93.33 % were considered valid according to the rules of the Bacterial Code, and they corresponded to 82.98 % of the total number of species validated between 2001 and 2018. Streptomyces, Bacillus and Paenibacillus each had more than 200 species described in the period. However, almost 40 % of all species were from the phylum Proteobacteria. Most bacteria were Gram-stain-negative, bacilli and isolated from soil. Thirteen species and one genus homonyms were found. With respect to methodologies of bacterial characterization, the use of terms related to 16S rRNA and polar lipids increased along these years, and terms related to genome metrics only began to appear from 2009 onward, although at a relatively lower frequency. Bacterial taxonomy is known as a conservative discipline, but it gradually changed in terms of players and practices. With the advent of the mandatory use of genomic analyses for species description, we are probably witnessing a turning point in the evolution of bacterial taxonomy.

Isolation and Characterization of Plant Growth-Promoting Endophytic Bacteria Paenibacillus polymyxa SK1 from Lilium lancifolium

Paenibacillus polymyxa is a plant growth-promoting rhizobacterium that has immense potential to be used as an environmentally friendly replacement of chemical fertilizers and pesticides. In the present study, Paenibacillus polymyxa SK1 was isolated from bulbs of Lilium lancifolium. The isolated endophytic strain showed antifungal activities against important plant pathogens like Botryosphaeria dothidea, Fusarium oxysporum, Botrytis cinerea, and Fusarium fujikuroi. The highest percentage of growth inhibition, i.e., 66.67 ± 2.23%, was observed for SK1 against Botryosphaeria dothidea followed by 61.19 ± 3.12%, 60.71 ± 3.53%, and 55.54 ± 2.89% against Botrytis cinerea, Fusarium fujikuroi, and Fusarium oxysporum, respectively. The metabolite profiling of ethyl acetate fraction was assessed through the UHPLC-LTQ-IT-MS/MS analysis, and putative identification was done with the aid of the GNPS molecular networking workflow. A total of 29 compounds were putatively identified which included dipeptides, tripeptides, cyclopeptides (cyclo-(Leu-Leu), cyclo(Pro-Phe)), 2-heptyl-3-hydroxy 4-quinolone, 6-oxocativic acid, anhydrobrazilic acid, 1-(5-methoxy-1H-indol-3-yl)-2-piperidin-1-ylethane-1,2-dione, octadecenoic acid, pyochelin, 15-hydroxy-5Z,8Z,11Z, 13E-eicosatetraenoic acid, (Z)-7-[(2R,3S)-3-[(2Z,5E)-Undeca-2,5-dienyl]oxiran-2-yl]hept-5-enoic acid, arginylasparagine, cholic acid, sphinganine, elaidic acid, gossypin, L-carnosine, tetrodotoxin, and ursodiol. The high antifungal activity of SK1 might be attributed to the presence of these bioactive compounds. The isolated strain SK1 showed plant growth-promoting traits such as the production of organic acids, ACC deaminase, indole-3-acetic acid (IAA), siderophores, nitrogen fixation, and phosphate solubilization. IAA production was strongly correlated with the application of exogenous tryptophan concentrations in the medium. Furthermore, inoculation of SK1 enhanced plant growth of two Lilium varieties, Tresor and White Heaven, under greenhouse condition. In the light of these findings, the P. polymyxa SK1 may be utilized as a source of plant growth promotion and disease control in sustainable agriculture.

Scientific Opinion on the update of the list of QPS-recommended biological agents intentionally added to food or feed as notified to EFSA (2017-2019)

The qualified presumption of safety (QPS) was developed to provide a safety pre-assessment within EFSA for microorganisms. Strains belonging to QPS taxonomic units (TUs) still require an assessment based on a specific data package, but QPS status facilitates fast track evaluation. QPS TUs are unambiguously defined biological agents assessed for the body of knowledge, their safety and their end use. Safety concerns are, where possible, to be confirmed at strain or product level, and reflected as 'qualifications'. Qualifications need to be evaluated at strain level by the respective EFSA units. The lowest QPS TU is the species level for bacteria, yeasts and protists/algae, and the family for viruses. The QPS concept is also applicable to genetically modified microorganisms used for production purposes if the recipient strain qualifies for the QPS status, and if the genetic modification does not indicate a concern. Based on the actual body of knowledge and/or an ambiguous taxonomic position, the following TUs were excluded from the QPS assessment: filamentous fungi, oomycetes, streptomycetes, Enterococcus faecium, Escherichia coli and bacteriophages. The list of QPS-recommended biological agents was reviewed and updated in the current opinion and therefore now becomes the valid list. For this update, reports on the safety of previously assessed microorganisms, including bacteria, yeasts and viruses (the latter only when used for plant protection purposes) were reviewed, following an Extensive Literature Search strategy. All TUs previously recommended for 2016 QPS list had their status reconfirmed as well as their qualifications. The TUs related to the new notifications received since the 2016 QPS opinion was periodically evaluated for QPS status in the Statements of the BIOHAZ Panel, and the QPS list was also periodically updated. In total, 14 new TUs received a QPS status between 2017 and 2019: three yeasts, eight bacteria and three algae/protists.

Update of the list of QPS-recommended biological agents intentionally added to food or feed as notified to EFSA 11: suitability of taxonomic units notified to EFSA until September 2019

Qualified presumption of safety (QPS) was developed to provide a generic safety evaluation for biological agents to support EFSA's Scientific Panels. The taxonomic identity, body of knowledge, safety concerns and antimicrobial resistance are assessed. Safety concerns identified for a taxonomic unit (TU) are where possible to be confirmed at strain or product level, reflected by 'qualifications'. No new information was found that would change the previously recommended QPS TUs and their qualifications. The list of microorganisms notified to EFSA was updated with 54 biological agents, received between April and September 2019; 23 already had QPS status, 14 were excluded from the QPS exercise (7 filamentous fungi, 6 Escherichia coli, Sphingomonas paucimobilis which was already evaluated). Seventeen, corresponding to 16 TUs, were evaluated for possible QPS status, fourteen of these for the first time, and Protaminobacter rubrum, evaluated previously, was excluded because it is not a valid species. Eight TUs are recommended for QPS status. Lactobacillus parafarraginis and Zygosaccharomyces rouxii are recommended to be included in the QPS list. Parageobacillus thermoglucosidasius and Paenibacillus illinoisensis can be recommended for the QPS list with the qualification 'for production purposes only' and absence of toxigenic potential. Bacillus velezensis can be recommended for the QPS list with the qualification 'absence of toxigenic potential and the absence of aminoglycoside production ability'. Cupriavidus necator, Aurantiochytrium limacinum and Tetraselmis chuii can be recommended for the QPS list with the qualification 'production purposes only'. Pantoea ananatis is not recommended for the QPS list due to lack of body of knowledge in relation to its pathogenicity potential for plants. Corynebacterium stationis, Hamamotoa singularis, Rhodococcus aetherivorans and Rhodococcus ruber cannot be recommended for the QPS list due to lack of body of knowledge. Kodamaea ohmeri cannot be recommended for the QPS list due to safety concerns.

Physiological response of North China red elder container seedlings to inoculation with plant growth-promoting rhizobacteria under drought stress

The issue of how to alleviate the negative effects imposed by water stress is an interesting problem. Plant growth-promoting rhizobacteria (PGPR) colonize the rhizosphere of plants and are known to promote the growth of crops. However, there are few studies characterizing the physiological response of plants to drought stress after PGPR inoculation. The aim of this study was to investigate the effectiveness of different PGPRs in arid environments and then investigated the effects of PGPR inoculation under drought stress on the physiological characteristics and growth of North China red elder (Sambucus williamsii) nursery container seedlings. The viable count of different PGPRs under drought stress varies widely, and the drought tolerance of Acinetobacter calcoaceticus X128 was significantly higher than that of other PGPRs. In comparison with non-inoculation, inoculation with X128 in an arid environment significantly increased stomatal conductance and mitigated the inhibition of net photosynthetic rate caused by drought stress; this mitigating effect of inoculation is enhanced as the level of drought stress increases. Relative to non-inoculated seedlings, cytokinin levels in the leaves increased by 91.17% under severe drought stress conditions in inoculated seedlings. However, X128 inoculation decreased this deficit to only 44.54%. Compared with non-inoculated seedlings, the relative water content of inoculated seedlings under severe drought stress increased by 15.06%, however the relative conductivity decreased by 12.48%. Consequently, X128 could increase dry matter accumulation of S. williamsii regardless of watering status, indicative of the greater benefits of PGPR on shoot growth than root. Therefore, inoculation of A. calcoaceticus X128 under drought conditions play a significant role for alleviating the negative effects imposed by water stress and promoting plant growth.

Characterization and Metabolism Effect of Seed Endophytic Bacteria Associated With Peanut Grown in South China

Endophytes are considered to be excellent biocontrol agents and biofertilizers, and are associated with plant growth promotion and health. In particular, seed-endophytic bacteria benefit the host plant’s progeny via vertical transmission, and can play a role in plant growth and defense. However, seed-associated endophytic bacteria have not been fully explored, with very little known about how they interact with peanut (Arachis hypogaea), for example. Here, 10 genera of endophytic bacteria were isolated from the root tips of peanut seedlings grown either aseptically or in soil. Forty-two bacterial colonies were obtained from peanut seedlings grown in soil, mostly from the genus Bacillus. Eight colonies were obtained from aseptic seedling root tips, including Bacillus sp., Paenibacillus sp., and Pantoea dispersa. Four Bacillus peanut strains GL1–GL4 (B.p.GL1-GL4) produced bio-films, while B.p.GL2 and Paenibacillus glycanilyticus YMR3 (P.g.YMR3) showed strong amylolytic capability, enhanced peanut biomass, and increased numbers of root nodules. Conversely, P. dispersa YMR1 (P.d.YMR1) caused peanut plants to wilt. P.g.YMR3 was distributed mainly around or inside vacuoles and was transmitted to the next generation through gynophores and ovules. Hexanoate, succinate, and jasmonic acid (JA) accumulated in peanut root tips after incubation with P.g.YMR3, but linolenate content decreased dramatically. This suggests that strain P.g.YMR3 increases JA content (14.93-fold change) and modulates the metabolism of peanut to facilitate nodule formation and growth. These findings provide new insight into plant–seed endophytic bacterial interactions in peanut.

Effect of the inoculation of plant growth-promoting rhizobacteria on the photosynthetic characteristics of Sambucus williamsii Hance container seedlings under drought stress

Plant growth-promoting rhizobacteria (PGPR) are beneficial bacteria that survive within the range of plant rhizosphere and can promote plant growth. The effects of PGPR in promoting plant growth, activating soil nutrients, reducing fertilizer application, and improving the resistance of plant inducible system have been widely investigated. However, few studies have investigated PGPR as elicitors of tolerance to abiotic stresses, especially drought stress. In this study, the effects of Acinetobacter calcoaceticus X128 on the photosynthetic rate (Pn), stomatal conductance (Gs), intracellular CO2 concentration (Ci), and total chlorophyll content [Chl(a+b)] of Sambucus williamsii Hance seedling leaves under moderate drought stress and drought-rewatering conditions were determined. Compared with those of uninoculated seedlings, the average Pn values during the entire drought stress of inoculated seedlings increased by 12.99%. As the drought duration was lengthened, Ci of uninoculated leaves continued to increase after rapidly declining, whereas Gs continuously decreased. Furthermore, their photosynthetic properties were simultaneously restricted by stomatal and non-stomatal factors. After X128 inoculation, Ci and Gs of S. williamsii Hance leaves continued to decrease, and their photosynthetic properties were mainly restricted by stomatal factors. At the end of the drought stress, water stress reduced [Chl(a + b)] of S. williamsii Hance leaves by 13.49%. However, X128 inoculation decreased this deficit to only 7.39%. After water supply was recovered, Pn, Gs, and [Chl(a+b)] in uninoculated leaves were reduced by 14.23%, 12.02%, and 5.86%, respectively, relative to those under well-watered conditions. However, Ci increased by 6.48%. Compared with those of uninoculated seedlings, Pn, Gs, and [Chl(a+b)] in X128-inoculated seedlings were increased by 9.83%, 9.30%, and 6.85%, respectively. Therefore, the inoculation of X128 under arid environments can mitigate the reduction of chlorophyll, delay the restriction caused by non-stomatal factors to Pn in plant leaves under water stress, and can be more conducive to the recovery of photosynthetic functions of leaves after water supply is recovered.

Impact of Elemental Sulfur on the Rhizospheric Bacteria of Durum Wheat Crop Cultivated on a Calcareous Soil

Previous experiments have shown that the application of fertilizer granules containing elemental sulfur (S0) as an ingredient (FBS0) in durum wheat crops produced a higher yield than that produced by conventional ones (F), provided that the soils of the experimental fields (F vs. FBS0) were of comparable quality and with the Olsen P content of the field's soil above 8 mg kg-1. In this experiment the FBS0 treatment took place in soil with Olsen P at 7.8 mg kg-1, compared with the F treatment's soil with Olsen P of 16.8 mg kg-1, aiming at reducing the imbalance in soil quality. To assess and evaluate the effect of FBS0 on the dynamics of the rhizospheric bacteria in relation to F, rhizospheric soil at various developmental stages of the crops was collected. The agronomic profile of the rhizospheric cultivable bacteria was characterized and monitored, in connection with the dynamics of phosphorus, iron, organic sulfur, and organic nitrogen, in both the rhizosoil and the aerial part of the plant during development. Both crops were characterized by a comparable dry mass accumulation per plant throughout development, while the yield of the FBS0 crop was 3.4% less compared to the F crop's one. The FBS0 crop's aerial part showed a transient higher P and Fe concentration, while its organic N and S concentrations followed the pattern of the F crop. The incorporation of S0 into the conventional fertilizer increased the percentage of arylsulfatase (ARS)-producing bacteria in the total bacterial population, suggesting an enhanced release of sulfate from the soil's organic S pool, which the plant could readily utilize. The proportion of identified ARS-producing bacteria possessing these traits exhibited a maximum value before and after topdressing. Phylogenetic analysis of the 68 isolated ARS-producing bacterial strains revealed that the majority of the isolates belonged to the Pseudomonas genus. A large fraction also possessed phosphate solubilization, and/or siderophore production, and/or ureolytic traits, thus improving the crop's P, Fe, S, and N balance. The aforementioned findings imply that the used FBS0 substantially improved the quality of the rhizosoil at the available phosphorus limiting level by modulating the abundance of the bacterial communities in the rhizosphere and effectively enhancing the microbially mediated nutrient mobilization towards improved plant nutritional dynamics.

Promising bacterial genera for agricultural practices: An insight on plant growth-promoting properties and microbial safety aspects

In order to address the ever-increasing problem of the world's population food needs, the optimization of farming crops yield, the combat of iron deficiency in plants (chlorosis) and the elimination/reduction of crop pathogens are of key challenges to solve. Traditional ways of solving these problems are either unpractical on a large scale (e.g. use of manure) or are not environmental friendly (e.g. application of iron-synthetic fertilizers or indiscriminate use of pesticides). Therefore, the search for greener substitutes, such as the application of siderophores of bacterial source or the use of plant-growth promoting bacteria (PGPB), is presented as a very promising alternative to enhance yield of crops and performance. However, the use of microorganisms is not a risk-free solution and the potential biohazards associated with the utilization of bacteria in agriculture should be considered. The present work gives a current overview of the main mechanisms associated with the use of bacteria in the promotion of plant growth. The potentiality of several bacterial genera (Azotobacter, Azospirillum, Bacillus, Pantoea, Pseudomonas and Rhizobium) regarding to siderophore production capacity and other plant growth-promoting properties are presented. In addition, the field performance of these bacteria genera as well as the biosafety aspects related with their use for agricultural proposes are reviewed and discussed.

Comparison of five bacterial strains producing siderophores with ability to chelate iron under alkaline conditions

Iron deficiency is one of the main causes of chlorosis in plants, which leads to losses in field crops quality and yield. The use of synthetic chelates to prevent or correct iron-deficiency is not satisfactory mainly due to their poor biodegradability. The present work aimed to search suitable microorganisms to produce alternative, environment-friendly iron-chelating agents (siderophores). For this purpose, the performance of five bacteria (Azotobacter vinelandii, Bacillus megaterium, Bacillus subtilis, Pantoea allii and Rhizobium radiobacter) was evaluated, regarding siderophore production kinetics, level of siderophore production (determined by chrome azurol S, CAS method), type of siderophore produced (using Arnow and Csaky's tests) and iron-chelating capacity at pH 9.0. All bacteria were in stationary phase at 24 h, except A. vinelandii (at 72 h) and produced the maximum siderophore amount (80-140 µmol L-1) between 24 and 48 h, with the exception of A. vinelandii (at 72 h). The analysis of culture filtrates revealed the presence of catechol-type siderophores for B. subtilis and R. radiobacter and hydroxamate-type siderophores for B. megaterium and P. allii. In the case of A. vinelandii, both siderophore-types (catechol and hydroxamates) were detected. The highest iron-chelating capacity, at pH 9.0, was obtained by B. megaterium followed by B. subtilis and A. vinelandii. Therefore, these three bacteria strains are the most promising bacteria for siderophore production and chlorosis correction under alkaline conditions.