Bacillus: A Biological Tool for Crop Improvement through Bio-Molecular Changes in Adverse Environments

Insights into endophytic bacterial diversity of rice grown across the different agro-ecological regions of West Bengal, India

Endophytes have recently garnered importance worldwide and multiple studies are being conducted to understand their important role and mechanism of interaction inside plants. But before we indulge in their functions it is necessary to dig into the microbiome. This will help to get a complete picture of the microbes intrinsic to their host and understand changes in community composition with respect to their habitats. To fulfil this requirement in our study we have attempted to dissect the endophytic diversity in roots of rice plant grown across the various agro-ecological zones of West Bengal by undergoing amplicon analysis of their 16S rRNA gene. Based on the measured environmental parameters agro-ecological zones can be divided into two groups: nutrient dense groups, representing zones like Gangetic, Northern hill and Terai-Teesta zone characterised by soil with higher levels of nitrogen (N) and total organic carbon and nutrient low groups representing Coastal saline, Red-laterite and Vindhyan zone mainly characterised by high electroconductivity and pH. Gammaproteobacteria, Alphaproteobacteria, Bacilli and Bacteroidetes were mostly abundant in nutrient dense sites whereas Clostridia and Planctomycetes were concentrated in nutrient low sites. Few genera (Aeromonas, Sulfurospirillum, Uliginosibacterium and Acidaminococcus) are present in samples cultivated in all the zones representing the core microbiome of rice in West Bengal, while some other genera like Lactococcus, Dickeya, Azonexus and Pectobacterium are unique to specific zone. Hence it can be concluded that this study has provided some insight in to the endophytic status of rice grown across the state of West Bengal.

Distribution, Genetic Diversity and Biocontrol of Aflatoxigenic Aspergillus flavus in Serbian Maize Fields

Maize is one of the leading export products in the Republic of Serbia. As a country where economic development depends on agriculture, maize production plays a critical role as a crop of strategic importance. Potential aflatoxin contamination of maize poses a risk to food and feed safety and tremendous economic losses. No aflatoxin contamination of maize samples harvested in 2019 and 2020 in different localities in the Republic of Serbia was detected by the Enzyme-Linked Immunosorbent Assay (ELISA) test and High-Performance Liquid Chromatography (HPLC) method. On the other hand, the Cluster Amplification Patterns (CAP) analyses of the isolated Aspergillus flavus strains from 2019 maize samples confirmed the presence of key biosynthesis genes responsible for aflatoxin production. Artificial inoculation and subsequent HPLC analysis of the inoculated maize samples confirmed the high capacity of the A. flavus strains for aflatoxin production, pointing to a high risk of contamination under favorable conditions. Prevention of aflatoxin contamination is primarily based on A. flavus control, where biocontrol agents play a significant role as sustainable disease management tools. In this study, antagonistic activity screening of the novel strains belonging to the Bacillus genus indicated superior suppression of A. flavus strains by two Bacillus strains isolated from the rhizosphere of Phaseolus vulgaris.

Draft genome sequencing and functional annotation and characterization of biofilm-producing bacterium Bacillus novalis PD1 isolated from rhizospheric soil

Biofilm forming bacterium Bacillus novalis PD1 was isolated from the rhizospheric soil of a paddy field. B. novalis PD1 is a Gram-positive, facultatively anaerobic, motile, slightly curved, round-ended, and spore-forming bacteria. The isolate B. novalis PD1 shares 98.45% similarity with B. novalis KB27B. B. vireti LMG21834 and B. drentensis NBRC 102,427 are the closest phylogenetic neighbours for B. novalis PD1. The draft genome RAST annotation showed a linear chromosome with 4,569,088 bp, encoding 6139 coding sequences, 70 transfer RNA (tRNA), and 11 ribosomal RNA (rRNA) genes. The genomic annotation of biofilm forming B. novalis PD1(> 3.6@OD_595nm) showed the presence of exopolysaccharide-forming genes (ALG, PSL, and PEL) as well as other biofilm-related genes (comER, Spo0A, codY, sinR, TasA, sipW, degS, and degU). Antibiotic inactivation gene clusters (ANT (6)-I, APH (3')-I, CatA15/A16 family), efflux pumps conferring antibiotic resistance genes (BceA, BceB, MdtABC-OMF, MdtABC-TolC, and MexCD-OprJ), and secondary metabolites linked to phenazine, terpene, and beta lactone gene clusters are part of the genome.

Transformation of Silver Nanoparticles (AgNPs) during Lime Treatment of Wastewater Sludge and Their Impact on Soil Bacteria

This study investigated the impact of lime stabilization on the fate and transformation of AgNPs. It also evaluated the changes in the population and diversity of the five most relevant bacterial phyla in soil after applying lime-stabilized sludge containing AgNPs. The study was performed by spiking an environmentally relevant concentration of AgNPs (2 mg AgNPs/g TS) in sludge, applying lime stabilization to increase pH to above 12 for two hours, and applying lime-treated sludge to soil samples. Transmission electron microscopy (TEM) and energy-dispersive X-ray spectroscopy (EDS) were used to investigate the morphological and compositional changes of AgNPs during lime stabilization. After the application of lime stabilized sludge to the soil, soil samples were periodically analyzed for total genomic DNA and changes in bacterial phyla diversity using quantitative polymerase chain reaction (qPCR). The results showed that lime treatment effectively removed AgNPs from the aqueous phase, and AgNPs were deposited on the lime molecules. The results revealed that AgNPs did not significantly impact the presence and diversity of the assessed phyla in the soil. However, lime stabilized sludge with AgNPs affected the abundance of each phylum over time. No significant effects on the soil total organic carbon (TOC), heterotrophic plate count (HPC), and percentage of the live cells were observed.

Stimulation of Nicotiana tabacum L. In Vitro Shoot Growth by Endophytic Bacillus cereus Group Bacteria

In vitro plant tissue cultures face various unfavorable conditions, such as mechanical damage, osmotic shock, and phytohormone imbalance, which can be detrimental to culture viability, growth efficiency, and genetic stability. Recent studies have revealed a presence of diverse endophytic bacteria, suggesting that engineering of the endophytic microbiome of in vitro plant tissues has the potential to improve their acclimatization and growth. Therefore, the aim of this study was to identify cultivated tobacco (Nicotiana tabacum L.) endophytic bacteria isolates that are capable of promoting the biomass accumulation of in vitro tobacco shoots. Forty-five endophytic bacteria isolates were obtained from greenhouse-grown tobacco plant leaves and were assigned to seven Bacillus spp. and one Pseudomonas sp. based on 16S rRNA or genome sequence data. To evaluate the bacterial effect on in vitro plant growth, tobacco shoots were inoculated with 22 isolates selected from distinct taxonomic groups. Four isolates of Bacillus cereus group species B. toyonensis, B. wiedmannii and B. mycoides promoted shoot growth by 11-21%. Furthermore, a contrasting effect on shoot growth was found among several isolates of the same species, suggesting the presence of strain-specific interaction with the plant host. Comparative analysis of genome assemblies was performed on the two closely related B. toyonensis isolates with contrasting plant growth-modulating properties. This revealed distinct structures of the genomic regions, including a putative enzyme cluster involved in the biosynthesis of linear azol(in)e-containing peptides and polysaccharides. However, the function of these clusters and their significance in plant-promoting activity remains elusive, and the observed contrasting effects on shoot growth are more likely to result from genomic sequence variations leading to differences in metabolic or gene expression activity. The Bacillus spp. isolates with shoot-growth-promoting properties have a potential application in improving the growth of plant tissue cultures in vitro.

Phytobeneficial and salt stress mitigating efficacy of IAA producing salt tolerant strains in Gossypium hirsutum

Salinity is one of the major agricultural concern that significantly limits the crop productivity. The plant growth promoting rhizobacteria (PGPR) may contribute in sustainable crop production under salt stress. The current study was designed to isolate the Indole Acetic Acid (IAA) producing salt tolerant PGPR to promote the growth of cotton (Gossypium hirsutum, FH-142) and induce its salt stress tolerance. Ten Salt Tolerant (ST) bacterial strains were screened for their PGP trait in vitro and evaluated for their beneficial effect on cotton plants growth by plant–microbe interaction assay in lab and under natural condition. GC–MS analysis of the metabolites of the selected bacterial strains confirmed the presence of indolic compounds like indole, indole-3-butyramide, benzylmalonic acid and 4-methyl-2-pyrrolidinone. The bacterial isolates ST4, ST5, ST6, ST15, ST16, ST17, ST18, ST20, ST22 and ST25 were identified as Bacillus sp., B. sonorensis, B. cereus, B. subtilis, Brevibacillus sp. B. safensis, B. paramycoides, Bacillus sp., B. cereus and B. tequilensis respectively on the basis of 16S rDNA sequencing. Bacteria inoculated plants had a significant (P < 0.05) increase in percentage germination up to (31%), root length (17%) and shoot length (34%) in lab while in wire house pot experiments, maximum enhancement in root length (31%) and shoot length (29%) was observed. ST bacterial strains inoculation improved the chlorophyll content index (34%), relative water content (36%), leaf area (33%), absorption of K⁺ (28%) and decreased the uptake of Na⁺ (58%) from soil in plants under salt stress over control in pot experiment. These ST PGPR have the potential to act as plant defense agents by enhancing plant growth, productivity, and tolerance in saline environment.

Combined application of two Bacillus species enhance phytoremediation potential of Brassica napus in an industrial metal-contaminated soil

This study aimed to assess the impact of individual as well as combined application of Lysinibacillus macroides and Bacillus safensis in phytoremediation potential of Brassica napus grown in soil contaminated by industrial effluents. In response to five metals; copper, chromium, nickel, lead, and cadmium, results revealed that germination percentage, fresh and dry weights, and photosynthetic pigments of B. napus decreased under contaminated soil. On the other hand, electrolyte leakage due to cellular injury, metabolites (proline and glycine betaine), antioxidant enzymes (superoxide dismutase, catalase, peroxidase, ascorbate peroxidase), accumulation of hydrogen peroxide and metals in plant's roots, shoots and leaves increased. Inoculation significantly reduced these effects as proved by the enhancement of germination percentage, fresh and dry biomass, and photosynthetic pigments. Simultaneously, the antioxidant enzymes, metabolites contents (proline and glycine betaine) and metal concentrations in plant's roots, shoots and leaves decreased. Combined application of both Bacilli strains was found more effective as compared to individual inoculation. It was concluded that metal resistant Bacillus species in combination had growth effects on B. napus and enhanced its phytoremediation efficiency in contaminated soil.Novelty statementBrassica napus; a hyper-accumulator of metals, loses phytoremediation potential with the passage of growth. Two Bacillus species (Lysinibacillus macroides and Bacillus safensis) having known bioremediation abilities were employed individually as well as in combination under metals contaminated soil to increase phytoremediation efficiency of B. napus. The metals containing soil used is a unique aspect in this study because selected soil, contaminated by industrial effluents, has not been evaluated or reported earlier. Combined application of Bacilli improved phytoremediation potential of B. napus more as compared to application of individual Bacillus strain which is yet another unique aspect of this investigation.

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.

Phyllosphere Community Assembly and Response to Drought Stress on Common Tropical and Temperate Forage Grasses

Grasslands represent a critical ecosystem important for global food production, soil carbon storage, and water regulation. Current intensification and expansion practices add to the degradation of grasslands and dramatically increase greenhouse gas emissions and pollution. Thus, new ways to sustain and improve their productivity are needed. Research efforts focus on the plant-leaf microbiome, or phyllosphere, because its microbial members impact ecosystem function by influencing pathogen resistance, plant hormone production, and nutrient availability through processes including nitrogen fixation. However, little is known about grassland phyllospheres and their response to environmental stress. In this study, globally dominant temperate and tropical forage grass species were grown in a greenhouse under current climate conditions and drought conditions that mimic future climate predictions to understand if (i) plant host taxa influence microbial community assembly, (ii) microbial communities respond to drought stress, and (iii) phyllosphere community changes correlate to changes in plant host traits and stress-response strategies. Community analysis using high-resolution sequencing revealed Gammaproteobacteria as the dominant bacterial class, which increased under severe drought stress on both temperate and tropical grasses while overall bacterial community diversity declined. Bacterial community diversity, structure, and response to drought were significantly different between grass species. This community dependence on plant host species correlated with differences in grass species traits, which became more defined under drought stress conditions, suggesting symbiotic evolutionary relationships between plant hosts and their associated microbial community. Further understanding these strategies and the functions microbes provide to plants will help us utilize microbes to promote agricultural and ecosystem productivity in the future. IMPORTANCE Globally important grassland ecosystems are at risk of degradation due to poor management practices compounded by predicted increases in severity and duration of drought over the next century. Finding new ways to support grassland productivity is critical to maintaining their ecological and agricultural benefits. Discerning how grassland microbial communities change in response to climate stress will help us understand how plant-microbe relationships may be useful to sustainably support grasslands in the future. In this study, phyllosphere community diversity and composition were significantly altered under drought conditions. The significance of our research is demonstrating how severe climate stress reduces bacterial community diversity, which previously was directly associated with decreased plant productivity. These findings guide future questions about functional plant-microbe interactions under stress conditions, greatly enhancing our understanding of how bacteria can increase food security by promoting grassland growth and resilience.

The application of Marinobacter hydrocarbonoclasticus as a bioaugmentation agent for the enhanced treatment of non-sterile fish wastewater

Wastewaters generated by fish processing are characterised by salt concentrations similar to or greater than that of seawater together with high nutrient concentrations (e.g. organic carbon and total nitrogen) due to the presence of blood, oil, and fish tissues. Fish processing wastewater entering rivers and oceans have become a key factor leading to the pollution of receiving waters; the adequate treatment of this wastewater is, therefore, crucial to a sustainable fish industry. The present study aimed to determine whether augmentation of fish wastewater with either Marinirhabdus sp., Marinobacter hydrocarbonoclasticus or a consortium of the two halobacteria, could successfully enhance the removal of both chemical oxygen demand (COD) and total nitrogen (TN) from fish wastewater. Following 9 days of incubation, the bioaugmentation treatment resulted in a significant reduction in COD, 88%, 91%, and 92% in fish wastewater augmented with either Marinirhabdus sp., Marinobacter hydrocarbonoclasticus respectively, or a consortium of the two halobacteria compared with the control (non-bioaugmented) treatment (77% removal). In tall bioaugmentation treatments (79-88%) TN removal was also significantly greater than the control treatment (57%). After 9 days of incubation, the COD and TN in bioaugmentation reached the European Union's (EU) wastewater discharge standard (Level B, COD < 120 mg L^-1, TN < 70 mg L^-1). The addition of monoculture was effective in enhancing the removal of COD, while co-culture significantly improved TN removal. Results of 16S rDNA sequence analysis investigating the survival of these introduced bacteria showed that only Marinobacter hydrocarbonoclasticus was detected at the end of the treatment, constituting 36% of the total bacterial population when added alone to the wastewater. This study confirms the effectiveness of bioaugmentation in removing COD and TN in saline fish wastewater. The ability of Marinobacter hydrocarbonclasticus to enhance the treatment and dominate the bacterial community suggests the commercial potential of this organism for bioaugmentation of aquaculture wastewater without the need for further bioaugmentation.

Microbial Biostimulants as Response to Modern Agriculture Needs: Composition, Role and Application of These Innovative Products

An increasing need for a more sustainable agriculturally-productive system is required in order to preserve soil fertility and reduce soil biodiversity loss. Microbial biostimulants are innovative technologies able to ensure agricultural yield with high nutritional values, overcoming the negative effects derived from environmental changes. The aim of this review was to provide an overview on the research related to plant growth promoting microorganisms (PGPMs) used alone, in consortium, or in combination with organic matrices such as plant biostimulants (PBs). Moreover, the effectiveness and the role of microbial biostimulants as a biological tool to improve fruit quality and limit soil degradation is discussed. Finally, the increased use of these products requires the achievement of an accurate selection of beneficial microorganisms and consortia, and the ability to prepare for future agriculture challenges. Hence, the implementation of the microorganism positive list provided by EU (2019/1009), is desirable.

Recent Advances in the Molecular Effects of Biostimulants in Plants: An Overview

As the world develops and population increases, so too does the demand for higher agricultural output with lower resources. Plant biostimulants appear to be one of the more prominent sustainable solutions, given their natural origin and their potential to substitute conventional methods in agriculture. Classified based on their source rather than constitution, biostimulants such as humic substances (HS), protein hydrolysates (PHs), seaweed extracts (SWE) and microorganisms have a proven potential in improving plant growth, increasing crop production and quality, as well as ameliorating stress effects. However, the multi-molecular nature and varying composition of commercially available biostimulants presents challenges when attempting to elucidate their underlying mechanisms. While most research has focused on the broad effects of biostimulants in crops, recent studies at the molecular level have started to unravel the pathways triggered by certain products at the cellular and gene level. Understanding the molecular influences involved could lead to further refinement of these treatments. This review comprises the most recent findings regarding the use of biostimulants in plants, with particular focus on reports of their molecular influence.

Screening of sunflower associated bacteria as biocontrol agents for plant growth promotion

Deleterious effects of artificially applied chemicals have highlighted the significance of biocontrol agents as suitable substitute for sustainable agriculture. In present study, three endophytic bacterial strains SV7, SV10 and LV19 showed extensive range of antifungal as well as plant growth promoting activities signifying potential to accomplish the requirement. Phylogenetic analysis revealed 100% similarity of three strains with taxon Firmicute. However, there was division among these isolates on basis of subgroups as SV7 belonged to Exiguobacterium auranticum, SV10 belonged to Paenibacillus sp. and LV19 was best fit in subgroup Priestia koreensis. All strains showed antifungal activity against Fusarium oxysporum on three different media (PDA, NA, LA) with maximum activity (53%) of LV19 strain on NA and least activity (13%) on PDA medium as recorded by zones of inhibition. In growth promotion experiments, combination of LV19 with Fusarium significantly suppressed chances of Fusarium wilt which is commonly caused by Fusarium oxysporum in sunflower plants. Diverse growth parameters (seed germination percentage, lengths and fresh weights of root and shoot) were significantly increased from 34 to 909% over pathogen infected plants only which was further proved by their root colonization analysis. Based on most efficient growth promotion by LV19 strain, expression of five plant defense related genes (SOD, PAL, NPR1, PR5, Chitinase) was evaluated revealing enhanced expression by 1.7-270-folds in consortium of LV19 and Fusarium. Thus, current study provided a scientific justification that bacterial strains in specific LV19 (Priestia koreensis) could be further developed as biocontrol agent with potential of plant growth promotion.

Antifungal Properties, Abiotic Stress Resistance, and Biocontrol Ability of Bacillus mojavensis PS17

Plant-protecting Bacillus sp. strains used as biocontrol agents frequently produce metabolites inhibiting phytopathogenic fungi. Recently, the search for a novel biocontrol agent with a wide spectrum of disease control drew attention to Bacillus subtilis and their related species, including Bacillus mojavensis. In this study, we determined the antifungal properties of the endophytic B. mojavensis PS17 isolated from wheat seeds. Metabolites produced by B. mojavensis PS-17 inhibit the growth of Fusarium graminearum, Fusarium oxysporum, Fusarium chlamydosporum, Ascochyta pisi, Alternaria alternate, Sclerotinia sclerotiorum, Verticillium dahliaee, and Epicoccum nigrum strains. B. mojavensis strain PS17 produces several hydrolytic enzymes, such as chitinase, β-glucanase, cellulase, lipase, and protease. Additionally, strain B. mojavensis PS17 demonstrates drought tolerance under osmotic pressure of -2.2 MPa and a moderate halotolerance in 5% (w/v) of NaCl. B. mojavensis PS17 on tomato seedlings was able to reduce lesions of Forl ZUM2407 by 48.11% ± 1.07, showing the potentials of B. mojavensis PS17 to be adapted as a biocontrol agent for agricultural use.

Bacillus velezensis strain MBY2, a potential agent for the management of crown gall disease

The reduction of the use chemical pesticides in agriculture is gaining importance as an objective of decision-makers in both politics and economics. Consequently, the development of technically efficient and economically affordable alternatives as, e.g., biological control agents or practices is highly solicited. Crown gall disease of dicotyledonous plants is caused by ubiquitous soil borne pathogenic bacteria of the Agrobacterium tumefaciens species complex, that comprises the species Agrobacterium fabrum and represents a globally relevant plant protection problem. Within the framework of a screening program for bacterial Agrobacterium antagonists a total of 14 strains were isolated from Tunisian soil samples and assayed for antagonistic activity against pathogenic agrobacteria. One particularly promising isolate, termed strain MBY2, was studied more in depth. Using a Multilocus Sequence Analysis (MLSA) approach, the isolate was assigned to the taxonomic species Bacillus velezensis. Strain MBY2 was shown to display antagonistic effects against the pathogenic A. fabrum strain C58 in vitro and to significantly decrease pathogen populations under sterile and non-sterile soil conditions as well as in the rhizosphere of maize and, to a lower extent, tomato plants. Moreover, the ability of B. velezensis MBY2 to reduce C58-induced gall development has been demonstrated in vivo on stems of tomato and almond plants. The present study describes B. velezensis MBY2 as a newly discovered strain holding potential as a biological agent for crown gall disease management.

An Exploration of Seaweed Polysaccharides Stimulating Denitrifying Bacteria for Safer Nitrate Removal

Excessive use of nitrogen fertilizer in intensively managed agriculture has resulted in abundant accumulation of nitrate in soil, which limits agriculture sustainability. How to reduce nitrate content is the key to alleviate secondary soil salinization. However, the microorganisms used in soil remediation cause some problems such as weak efficiency and short survival time. In this study, seaweed polysaccharides were used as stimulant to promote the rapid growth and safer nitrate removal of denitrifying bacteria. Firstly, the growth rate and NO₃⁻-N removal capacity of three kinds of denitrifying bacteria, Bacillus subtilis (BS), Pseudomonas stutzeri (PS) and Pseudomonas putida (PP), were compared. The results showed that Bacillus subtilis (BS) had a faster growth rate and stronger nitrate removal ability. We then studied the effects of Enteromorpha linza polysaccharides (EP), carrageenan (CA), and sodium alginate (AL) on growth and denitrification performance of Bacillus subtilis (BS). The results showed that seaweed polysaccharides obviously promoted the growth of Bacillus subtilis (BS), and accelerated the reduction of NO₃⁻-N. More importantly, the increased NH₄⁺-N content could avoid excessive loss of nitrogen, and less NO₂⁻-N accumulation could avoid toxic effects on plants. This new strategy of using denitrifying bacteria for safely remediating secondary soil salinization has a great significance.

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.

Antifungal mechanism of Bacillus amyloliquefaciens strain GKT04 against Fusarium wilt revealed using genomic and transcriptomic analyses

The application of endophytic bacteria, particularly members of the genus Bacillus, offers a promising strategy for the biocontrol of plant fungal diseases, owing to their sustainability and ecological safety. Although multiple secondary metabolites that demonstrate antifungal capacity have been identified in diverse endophytic bacteria, the regulatory mechanisms of their biosynthesis remain largely unknown. To elucidate this, we sequenced the entire genome of Bacillus amyloliquefaciens GKT04, a strain isolated from banana root, which showed high inhibitory activity against Fusarium oxysporum f. sp. cubense race 4 (FOC4). The GKT04 genome consists of a circular chromosome and a circular plasmid, which harbors 4,087 protein‐coding genes and 113 RNA genes. Eight gene clusters that could potentially encode antifungal components were identified. We further applied RNA‐Seq analysis to survey genome‐wide changes in the gene expression of strain GKT04 during its inhibition of FOC4. In total, 575 upregulated and 242 downregulated genes enriched in several amino acid and carbohydrate metabolism pathways were identified. Specifically, gene clusters associated with difficidin, bacillibactin, and bacilysin were significantly upregulated, and their gene regulatory networks were constructed. Our work thereby provides insights into the genomic features and gene expression patterns of this B. amyloliquefaciens strain, which presents an excellent potential for the biocontrol of Fusarium wilt.

Production, Purification, and Characterization of Bacillibactin Siderophore of Bacillus subtilis and Its Application for Improvement in Plant Growth and Oil Content in Sesame

Siderophores are low molecular weight secondary metabolites produced by microorganisms under low iron stress as a specific iron chelator. In the present study, a rhizospheric bacterium was isolated from the rhizosphere of sesame plants from Salem district, Tamil Nadu, India and later identified as Bacillus subtilis LSBS2. It exhibited multiple plant-growth-promoting (PGP) traits such as hydrogen cyanide (HCN), ammonia, and indole acetic acid (IAA), and solubilized phosphate. The chrome azurol sulphonate (CAS) agar plate assay was used to screen the siderophore production of LSBS2 and quantitatively the isolate produced 296 mg/L of siderophores in succinic acid medium. Further characterization of the siderophore revealed that the isolate produced catecholate siderophore bacillibactin. A pot culture experiment was used to explore the effect of LSBS2 and its siderophore in promoting iron absorption and plant growth of Sesamum indicum L. Data from the present study revealed that the multifarious Bacillus sp. LSBS2 could be exploited as a potential bioinoculant for growth and yield improvement in S. indicum.

Endophytic Strain Bacillus subtilis 26D Increases Levels of Phytohormones and Repairs Growth of Potato Plants after Colorado Potato Beetle Damage

Plant damage caused by defoliating insects has a long-term negative effect on plant growth and productivity. Consequently, the restoration of plant growth after exposure to pathogens or pests is the main indicator of the effectiveness of the implemented defense reactions. A short-term Leptinotarsa decemlineata Say attack on potato tube-grown plantlets (Solanum tuberosum L.) led to a reduction of both the length and mass of the shoots in 9 days. The decrease of the content of phytohormones—indole-3-acetic acid (IAA), abscisic acid (ABA), zeatin and zeatin–riboside—in shoots of damaged potato plants was found. Endophytic strain Bacillus subtilis 26D (Cohn) is capable of secreting up to 83.6 ng/mL IAA and up to 150 ng/mL cytokinins into the culture medium. Inoculation of potato plants with cells of the B. subtilis 26D increases zeatin–riboside content in shoots and the mass of roots of undamaged plants, but does not influence content of IAA and ABA and growth of shoots. The presence of B. subtilis 26D in plant tissues promoted a rapid recovery of the growth rates of shoots, as well as the wet and dry mass of roots of plants after the pest attack, which we associate with the maintenance of a high level of IAA, ABA and cytokinins in their tissues.

Efficacy of Indole Acetic Acid and Exopolysaccharides-Producing Bacillus safensis Strain FN13 for Inducing Cd-Stress Tolerance and Plant Growth Promotion in Brassica juncea (L.)

Untreated wastewater used for irrigating crops is the major source of toxic heavy metals and other pollutants in soils. These heavy metals affect plant growth and deteriorate the quality of edible parts of growing plants. Phytohormone (IAA) and exopolysaccharides (EPS) producing plant growth-promoting rhizobacteria can reduce the toxicity of metals by stabilizing them in soil. The present experiment was conducted to evaluate the IAA and EPS-producing rhizobacterial strains for improving growth, physiology, and antioxidant activity of Brassica juncea (L.) under Cd-stress. Results showed that Cd-stress significantly decreased the growth and physiological parameters of mustard plants. Inoculation with Cd-tolerant, IAA and EPS-producing rhizobacterial strains, however, significantly retrieved the inhibitory effects of Cd-stress on mustard growth, and physiology by up regulating antioxidant enzyme activities. Higher Cd accumulation and proline content was observed in the roots and shoot tissues upon Cd-stress in mustard plants while reduced proline and Cd accumulation was recorded upon rhizobacterial strains inoculation. Maximum decrease in proline contents (12.4%) and Cd concentration in root (26.9%) and shoot (29%) in comparison to control plants was observed due to inoculation with Bacillus safensis strain FN13. The activity of antioxidant enzymes was increased due to Cd-stress; however, the inoculation with Cd-tolerant, IAA-producing rhizobacterial strains showed a non-significant impact in the case of the activity of superoxide dismutase (SOD), peroxidase (POX) and catalase (CAT) in Brassica juncea (L.) plants under Cd-stress. Overall, Bacillus safensis strain FN13 was the most effective strain in improving the Brassica juncea (L.) growth and physiology under Cd-stress. It can be concluded, as the strain FN13 is a potential phytostabilizing biofertilizer for heavy metal contaminated soils, that it can be recommended to induce Cd-stress tolerance in crop plants.

Rhizosphere community selection reveals bacteria associated with reduced root disease

BACKGROUND

Microbes benefit plants by increasing nutrient availability, producing plant growth hormones, and protecting against pathogens. However, it is largely unknown how plants change root microbial communities.

RESULTS

In this study, we used a multi-cycle selection system and infection by the soilborne fungal pathogen Rhizoctonia solani AG8 (hereafter AG8) to examine how plants impact the rhizosphere bacterial community and recruit beneficial microorganisms to suppress soilborne fungal pathogens and promote plant growth. Successive plantings dramatically enhanced disease suppression on susceptible wheat cultivars to AG8 in the greenhouse. Accordingly, analysis of the rhizosphere soil microbial community using deep sequencing of 16S rRNA genes revealed distinct bacterial community profiles assembled over successive wheat plantings. Moreover, the cluster of bacterial communities formed from the AG8-infected rhizosphere was distinct from those without AG8 infection. Interestingly, the bacterial communities from the rhizosphere with the lowest wheat root disease gradually separated from those with the worst wheat root disease over planting cycles. Successive monocultures and application of AG8 increased the abundance of some bacterial genera which have potential antagonistic activities, such as Chitinophaga, Pseudomonas, Chryseobacterium, and Flavobacterium, and a group of plant growth-promoting (PGP) and nitrogen-fixing microbes, including Pedobacter, Variovorax, and Rhizobium. Furthermore, 47 bacteria isolates belong to 35 species were isolated. Among them, eleven and five exhibited antagonistic activities to AG8 and Rhizoctonia oryzae in vitro, respectively. Notably, Janthinobacterium displayed broad antagonism against the soilborne pathogens Pythium ultimum, AG8, and R. oryzae in vitro, and disease suppressive activity to AG8 in soil.

CONCLUSIONS

Our results demonstrated that successive wheat plantings and pathogen infection can shape the rhizosphere microbial communities and specifically accumulate a group of beneficial microbes. Our findings suggest that soil community selection may offer the potential for addressing agronomic concerns associated with plant diseases and crop productivity. Video Abstract.

Multifaceted intervention of Bacillus spp. against salinity stress and Fusarium wilt in tomato

AIM

This study aimed to screen halotolerant Bacillus strains able to promote growth and protect tomato plants against salt stress and Fusarium wilt (Fusarium oxysporum f. sp. lycopersici).

METHODS AND RESULTS

We evaluated some halotolerant strains of Bacillus spp. (Bacillus velezensis (AP-3) and Bacillus spp. (AP-6, AP-85 and AP-100)) to promote growth of tomato plants grown under salinity stress conditions and to protect them against Fusarium wilt disease. Such strains had been previously selected among 154 bacterial strains through biochemical tests (siderophores and indoleacetic acid productions, cellulase and catalase activity, nitrogen fixation and phosphate solubilization) in the presence of 100-mmol l^-1 NaCl. Besides the above-mentioned strains, B. subtilis QST-713 (Serenade^TM ) was also evaluated. Compared to control plants, aboveground dry weight increased in plants inoculated with AP-6, AP-85, AP-3, AP-100 and QST-713 strains developed in the absence of salt stress. The same tendency occurred for root dry weight; however, AP-3 strain was more effective, promoting an increase of 163%, when compared to control. Chlorophyll index and height increased >40 and 53%, respectively, for all Bacillus strains. Saline stress reduced plant growth regardless of the presence of Bacillus. Height, stem diameter, and aboveground and root dry weights increased in plants treated with Bacillus strains grown under saline conditions when compared to control. Bacillus velezensis AP-3 reduced the severity of Fusarium wilt in tomato by 50% when compared to control.

CONCLUSION

Halotolerant Bacillus strains controlled tomato Fusarium wilt, increased growth as well as tolerance to salt stress.

SIGNIFICANCE AND IMPACT OF THE STUDY

We demonstrated the efficacy of halotolerant Bacillus strains to control Fusarium wilt and improve tomato growth. We also demonstrated that these Bacillus strains protect tomato plants against salt stress. Bacillus can be used in an eco-friendly way because they are considered Generally Recognized As Safe.

Biochemical mechanisms of rhizospheric Bacillus subtilis-facilitated phytoextraction by alfalfa under cadmium stress - Microbial diversity and metabolomics analyses

The effects of Bacillus subtilis inoculation on the growth and Cd uptake of alfalfa were evaluated in this research using pot experiments, and the relevant biochemical mechanisms were first investigated by combined microbial diversity and nontarget metabolomics analyses. The results indicated that inoculation with alfalfa significantly decreased the amount of plant malondialdehyde (MDA) and improved the activities of plant antioxidant enzymes and soil nutrient cycling-involved enzymes, thereby promoting biomass by 29.4%. Inoculation also increased Cd bioavailability in rhizosphere soil by 12.0% and Cd removal efficiency by 139.3%. The biochemical mechanisms included enhanced bacterial diversity, transformed microbial community composition, regulated amounts of amino acids, fatty acids, carbohydrates, flavonoids and phenols in rhizosphere soil metabolites, and modulations of the corresponding Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. These responses were beneficial to microbial activity, nutrient cycling, and Cd mobilization, detoxification, and decontamination by alfalfa in soil. This study, especially the newly identified differential metabolites and metabolic pathways, provides new insights into mechanism revelation and strategy development in microbe-assisted phytomanagement of heavy metal-contaminated soils.

Sucrose triggers a novel signaling cascade promoting Bacillus subtilis rhizosphere colonization

Beneficial rhizobacteria promote plant growth and protect plants against phytopathogens. Effective colonization on plant roots is critical for the rhizobacteria to exert beneficial activities. How bacteria migrate swiftly in the soil of semisolid or solid nature remains unclear. Here we report that sucrose, a disaccharide ubiquitously deployed by photosynthetic plants for fixed carbon transport and storage, and abundantly secreted from plant roots, promotes solid surface motility (SSM) and root colonization by Bacillus subtilis through a previously uncharacterized mechanism. Sucrose induces robust SSM by triggering a signaling cascade, first through extracellular synthesis of polymeric levan, which in turn stimulates strong production of surfactin and hyper-flagellation of the cells. B. subtilis poorly colonizes the roots of Arabidopsis thaliana mutants deficient in root-exudation of sucrose, while exogenously added sucrose selectively shapes the rhizomicrobiome associated with the tomato plant roots, promoting specifically bacilli and pseudomonad. We propose that sucrose activates a signaling cascade to trigger SSM and promote rhizosphere colonization by B. subtilis. Our findings also suggest a practicable approach to boost prevalence of beneficial Bacillus species in plant protection.

Plant Growth-Promoting Bacteria as an Emerging Tool to Manage Bacterial Rice Pathogens

As a major food crop, rice (Oryza sativa) is produced and consumed by nearly 90% of the population in Asia with less than 9% produced outside Asia. Hence, reports on large scale grain losses were alarming and resulted in a heightened awareness on the importance of rice plants' health and increased interest against phytopathogens in rice. To serve this interest, this review will provide a summary on bacterial rice pathogens, which can potentially be controlled by plant growth-promoting bacteria (PGPB). Additionally, this review highlights PGPB-mediated functional traits, including biocontrol of bacterial rice pathogens and enhancement of rice plant's growth. Currently, a plethora of recent studies address the use of PGPB to combat bacterial rice pathogens in an attempt to replace existing methods of chemical fertilizers and pesticides that often lead to environmental pollutions. As a tool to combat bacterial rice pathogens, PGPB presented itself as a promising alternative in improving rice plants' health and simultaneously controlling bacterial rice pathogens in vitro and in the field/greenhouse studies. PGPB, such as Bacillus, Pseudomonas, Enterobacter, Streptomyces, are now very well-known. Applications of PGPB as bioformulations are found to be effective in improving rice productivity and provide an eco-friendly alternative to agroecosystems.

Cadmium toxicity in plants: Impacts and remediation strategies

Cadmium (Cd) is an unessential trace element in plants that is ubiquitous in the environment. Anthropogenic activities such as disposal of urban refuse, smelting, mining, metal manufacturing, and application of synthetic phosphate fertilizers enhance the concentration of Cd in the environment and are carcinogenic to human health. In this manuscript, we reviewed the sources of Cd contamination to the environment, soil factors affecting the Cd uptake, the dynamics of Cd in the soil rhizosphere, uptake mechanisms, translocation, and toxicity of Cd in plants. In crop plants, the toxicity of Cd reduces uptake and translocation of nutrients and water, increases oxidative damage, disrupts plant metabolism, and inhibits plant morphology and physiology. In addition, the defense mechanism in plants against Cd toxicity and potential remediation strategies, including the use of biochar, minerals nutrients, compost, organic manure, growth regulators, and hormones, and application of phytoremediation, bioremediation, and chemical methods are also highlighted in this review. This manuscript may help to determine the ecological importance of Cd stress in interdisciplinary studies and essential remediation strategies to overcome the contamination of Cd in agricultural soils.

Effect of Bacillus subtilis on antioxidant enzyme activities in tomato grafting

Grafting generally means stress to a plant and this triggers antioxidant defense systems. An imbalance in reactive oxygen species may negatively affect the grafting success. Several research projects have studied the association with plant growth-promoting rhizobacteria (PGPR) and it has been documented that they enhance nutrient acquisition, regulate hormone levels, and influence the antioxidant response in crops. However, little is known about the strategy of inoculating grafted herbaceous plants with PGPR and its effect on the antioxidant response. The effects of inoculating a strain of Bacillus subtilis on the antioxidant metabolism of grafted tomato were evaluated. In this study, two different rootstocks were used for tomato (Solanum lycopersicum L. var. Rio Grande (RG)): [S. lycopersicum L. var. cerasiforme (Ch)] and eggplant [(Solanum melanogena L. (Ber)] to establish a compatible graft (RGCh) and a semicompatible graft (RGBer). Enzyme activities involved in the antioxidant defense system: superoxide dismutase (SOD), catalase (CAT), phenylalanine ammonia lyase (PAL), polyphenol oxidase (PPO), peroxidase (POD), and total phenols were measured during 4 weeks after grafting. The results show that for RGCh, during the first two weeks after grafting, the tendency was a decrease of the enzyme activity for SOD, CAT, PAL when inoculated with B. subtilis; while in the semicompatible graft RGBer, PPO and PAL decreased their activity after inoculation. For both combinations, the quantity of total phenols varied depending on the day. In both graft combinations, applications of B. subtilis resulted in 86 and 80% callusing compared with the uninoculated control where the percentages were 74 and 70% for RGCh and RGBer, respectively. The highest significant graft success (95%) was recorded 28 days after grafting for inoculated RGBer. These findings imply that B. subtilis induced antioxidant mechanisms in grafted plants and suggest that inoculation with this growth-promoting bacterium can represent a biotechnological approach to improve success in tomato grafting.

Facets of rhizospheric microflora in biocontrol of phytopathogen Macrophomina phaseolina in oil crop soybean

The use of microbial bioinoculants for managing plant diseases and promoting plant growth is an effective alternative approach to integrated farming. One of the devastating phytopathogens is Macrophomina phaseolina (Tassi) Goid. It is an omnipresent fungus infecting more than 500 plant species. It causes charcoal rot disease in soybean leading to 30-50% yield loss. Soybean Glycine max (L.) oil seed crop produced globally is highly susceptible to M. phaseolina. India is the fifth largest producer of soybean in the world. Madhya Pradesh is the largest soybean-producing state in India; Around 70% yield loss of soybean is accounted to M. phaseolina infection in India. Control of charcoal rot is the requisite of the current situation. Chemical control is not feasible due to saprophytic nature and prolonged survival of Macrophomina phaseolina. Chemical fungicides are expensive, toxic, hazardous, and cause pollution. Biological control is an effective approach to control this devastating fungus. The rhizosphere of soil is rich in beneficial microflora competent to suppress plant pathogens and also promote plant growth. PGPR have well-developed mechanisms that impart antagonistic traits to them. PGPR produces various antifungal metabolites siderophores and HCN which inhibit fungal growth, and can be used as potent BCA. Pseudomonas and Bacillus species have been reported effective against M. phaseolina. The mechanisms and antifungal compounds produced by these bacteria to control charcoal rot can be studied extensively. BCA or the metabolites secreted by them have the potential to develop effective bioformulations for soybean at the commercial level for sustainable agriculture.

Bacteria as Biocontrol Tool against Phytoparasitic Nematodes

Phytoparasitic nematodes cause severe damage and yield losses to numerous agricultural crops. Considering the revision of the EU legislation on the use of pesticides on agricultural crops, control strategies with low environmental impact are required. The approach based on the use of bacteria seems particularly promising as it also helps to reduce the applied amounts of chemicals and stabilize ecological changes. This paper gives an overview of the main types of bacteria that can be used as biological control agents against plant parasitic nematodes and their interrelationships with plants and other organisms. Many experiments have given positive results of phytoparasitic nematode control by bacteria, showing possible prospects for their application. In vitro, greenhouse and field experiments have shown that bacteria can regulate the development of ecto- and endoparasitic nematodes by different modes of action. Triggering the induction of plant defense mechanisms by bacteria is seen as the optimum tool because the efficacy of bacterial treatment can be higher than that of chemical pesticides or at least close to it. Moreover, bacterial application produces additional positive effects on growth stimulation, raises yields and suppresses other pathogenic microorganisms. Commercial formulations, both as single bacterial strains and bacterial complexes, are examined.

Comparative genomics analysis of two banana Fusarium wilt biocontrol endophytes Bacillus subtilis R31 and TR21 provides insights into their differences on phytobeneficial trait

Fusarium wilt of banana is considered one of the most destructive plant diseases. Bacillus subtilis R31 and TR21, isolated from Dendrobium sp. leaves, exhibit different phytobeneficial effects on banana Fusarium wilt bio-controlling. Here, we performed genome sequencing and comparative genomics analysis of R31 and TR21 to enhance our understanding of the different phytobeneficial traits. These results revealed that the strain-specific genes of R31 involved in sporulation, quorum sensing, and antibiotic synthesis allow R31 to present a better capacity of sporulation, rhizosphere adaptation, and quorum sensing than TR21. Selective pressure analysis indicated that the glycosylase and endo-alpha-(1- > 5)-L-arabinanase genes were strong positive selected, which may contribute to the TR21 to colonize well in banana's vascular bundles. Altogether, our findings presented here should advance further agricultural application of R31 and TR21 as two promising resources of plant growth promotion and biological control via genetic engineering.

Microbes as Biofertilizers, a Potential Approach for Sustainable Crop Production

Continuous decline of earth’s natural resources and increased use of hazardous chemical fertilizers pose a great concern for the future of agriculture. Biofertilizers are a promising alternative to hazardous chemical fertilizers and are gaining importance for attaining sustainable agriculture. Biofertilizers play a key role in increasing crop yield and maintaining long-term soil fertility, which is essential for meeting global food demand. Microbes can interact with the crop plants and enhance their immunity, growth, and development. Nitrogen, phosphorous, potassium, zinc, and silica are the essential nutrients required for the proper growth of crops, but these nutrients are naturally present in insolubilized or complex forms. Certain microorganisms render them soluble and make them available to the plants. The potential microbes, their mode of action, along with their effect on crops, are discussed in this review. Biofertilizers, being cost effective, non-toxic, and eco-friendly, serve as a good substitute for expensive and harmful chemical fertilizers. The knowledge gained from this review can help us to understand the importance of microbes in agriculture and the ways to formulate these microbes as biofertilizers for sustainable crop production.

Metagenomics and Culture Dependent Insights into the Distribution of Firmicutes across Two Different Sample Types Located in the Black Hills Region of South Dakota, USA

Firmicutes is almost a ubiquitous phylum. Several genera of this group, for instance, Geobacillus, are recognized for decomposing plant organic matter and for producing thermostable ligninolytic enzymes. Amplicon sequencing was used in this study to determine the prevalence and genetic diversity of the Firmicutes in two distinctly related environmental samples—South Dakota Landfill Compost (SDLC, 60 °C), and Sanford Underground Research Facility sediments (SURF, 45 °C). Although distinct microbial community compositions were observed, there was a dominance of Firmicutes in both the SDLC and SURF samples, followed by Proteobacteria. The abundant classes of bacteria in the SDLC site, within the phylum Firmicutes, were Bacilli (83.2%), and Clostridia (2.9%). In comparison, the sample from the SURF mine was dominated by the Clostridia (45.8%) and then Bacilli (20.1%). Within the class Bacilli, the SDLC sample had more diversity (a total of 11 genera with more than 1% operational taxonomic unit, OTU). On the other hand, SURF samples had just three genera, about 1% of the total population: Bacilli, Paenibacillus, and Solibacillus. With specific regard to Geobacillus, it was found to be present at a level of 0.07% and 2.5% in SURF and SDLC, respectively. Subsequently, culture isolations of endospore-forming Firmicutes members from these samples led to the isolation of a total of 117 isolates. According to colony morphologies, and identification based upon 16S rRNA and gyrB gene sequence analysis, we obtained 58 taxonomically distinct strains. Depending on the similarity indexes, a gyrB sequence comparison appeared more useful than 16S rRNA sequence analysis for inferring intra- and some intergeneric relationships between the isolates.

Bacillus circulans GN03 Alters the Microbiota, Promotes Cotton Seedling Growth and Disease Resistance, and Increases the Expression of Phytohormone Synthesis and Disease Resistance-Related Genes

Plant growth-promoting bacteria (PGPB) are components of the plant rhizosphere that promote plant growth and/or inhibit pathogen activity. To explore the cotton seedlings response to Bacillus circulans GN03 with high efficiency of plant growth promotion and disease resistance, a pot experiment was carried out, in which inoculations levels of GN03 were set at 10⁴ and 10⁸ cfu^⋅mL^-1. The results showed that GN03 inoculation remarkably enhanced growth promotion as well as disease resistance of cotton seedlings. GN03 inoculation altered the microbiota in and around the plant roots, led to a significant accumulation of growth-related hormones (indole acetic acid, gibberellic acid, and brassinosteroid) and disease resistance-related hormones (salicylic acid and jasmonic acid) in cotton seedlings, as determined with ELISA, up-regulated the expression of phytohormone synthesis-related genes (EDS1, AOC1, BES1, and GA20ox), auxin transporter gene (Aux1), and disease-resistance genes (NPR1 and PR1). Comparative genomic analyses was performed between GN03 and four similar species, with regards to phenotype, biochemical characteristics, and gene function. This study provides valuable information for applying the PGPB alternative, GN03, as a plant growth and disease-resistance promoting fertilizer.

Arbuscular Mycorrhizal Fungi (Rhizophagus clarus) and Rhizobacteria (Bacillus subtilis) Can Improve the Clonal Propagation and Development of Teak for Commercial Plantings

The Tectona grandis L.f. (teak) is an important forest species with high economy value in Asia, Africa, and Latin America. In Latin America, Brazil is one of the countries with the most cultivated areas. The cultivation of teak turns out to be challenging because of its high nutritional demand and the need for seedling production by clonal propagation that includes about 90 days in the nursery phase. The optimization of seedling production is necessary for better results in the nursery and to enhance growth in the field. In this way, the well-known advantage of using microorganisms that promote plant development appears as a potential biotechnological approach to be explored and for the implantation of new areas of wood production. In this study, the inoculation of Bacillus subtilis as plant growth-promoting rhizobacteria (PGPR) was evaluated, and Rhizophagus clarus, an arbuscular mycorrhizal fungus (AMF), and the co-inoculation of these microorganisms in the teak seedling production phase can improve the development of commercial plantations under field conditions. Experiments were carried out under greenhouse and field conditions to evaluate four treatments based on the substrate inoculation of the seedlings. Treatments consisted of a non-inoculated control, PGPR inoculation, AMF inoculation, and PGPR + AMF inoculation. The results of the biometric evaluation of seedlings in the greenhouse showed that there was a significant difference in AMF inoculation and PGPR + AMF inoculation in terms of the specific root length and root density treatments, there was also a positive correlation between these two treatments and the absorption of some nutrients, such as P, N, K, Mg, Cu, Mn, and Zn. This response led to an increase between 4.75 and 11.04% in the field growth rate.

Impact of anaerobically digested silver and copper oxide nanoparticles in biosolids on soil characteristics and bacterial community

This study investigated whether 2 and 30 mg AgNPs or CuONPs/g TS present in treated sludge (biosolids) may impact the soil health by monitoring the soil characteristics and soil bacterial community for 105 days after the application of biosolids. AgNPs or CuONPs/g TS were first anaerobically digested with mixed primary and secondary sludge rather than adding pristine nanoparticles to biosolids directly. Both environmentally relevant (under the USEPA ceiling concentration limits) and high concentrations of AgNPs and CuONPs were tested. Soil tests included TOC, TN, TP, pH, cell viability and heterotrophic plate counts (HPC). Metagenomic data was generated by high-throughput sequencing of the 16S rRNA gene to explore bacterial populations and diversity. AgNPs and CuONPs at 2 and 30 mg NPs/g TS of sludge could impact soil health factors such as bacterial diversity, community structure, and the population of plant growth-promoting rhizobacteria (PGPR). The population of the highly abundant bacteria that have important physiological roles in soil decreased, while the less important bacteria for soil function were able to thrive. CuONPs exhibited a higher level of toxicity than the AgNPs at both phylum and genus taxonomic levels, and the HPC decreased with higher concentrations of AgNPs and CuONPs. Initially, most of the studied phyla abundance was affected, but the control and other reactors approached similar levels by the end of the experiments, which may be explained by the decrease in toxicity due to the transformation of nanoparticles and the defence mechanisms of bacteria, and indicates the need for long-term field studies.

Antimicrobial Activity Against Phytopathogens and Inhibitory Activity on Solanine in Potatoes of the Endophytic Bacteria Isolated From Potato Tubers

As an important global crop, the potato (Solanum tuberosum L.) contains the endotoxin solanine that leads to human poisoning and major economic losses. Poisoning symptoms and even acute poisoning may occur when the content of solanine in potatoes exceeds 200 mg/kg. In addition, potatoes are susceptible to some pathogenic bacteria, including Streptomyces scabies and Erwinia carotovora subsp. atroseptica (Van Hall) dye, which can cause potato scab and potato blackleg disease, respectively. In this study, 37 culturable endophytic bacteria strains were obtained from potato tubers based on the culture-dependent method. Results indicated that nine strains showed antimicrobial activity against at least one pathogen by antimicrobial activity screening and 23 strains showed inhibitory activity on solanine in potato tubers. Among them, strain P-NA2-14 (Bacillus megaterium NBRC 15308T, 99.31%) showed not only better antimicrobial activity against both the two indicator pathogens, but also the best inhibitory activity on solanine, which was proved to be a potential biocontrol bacterium. Meanwhile, the relationship between the distribution of the endophytic bacterial community and the content of solanine in potato tubers was studied by Illumina-based analysis, indicating that the distribution of the endophytic bacterial community was obviously influenced by the content of solanine. The results showed a new insight into the relationship between plant secondary metabolites and endophytic bacteria in potato tubers and provided potential new technical support for the biological control of potato storage.

Biocontrol and plant growth-promoting potentiality of bacteria isolated from compost extract

The use of compost extracts is steadily increasing, offering an attractive way for plant growth enhancement and disease management replacing chemical pesticides. In this study, potential mechanisms involved in plant growth promotion and suppressive activity against fungal diseases, of a compost extract produced from poultry manure/olive husk compost, were investigated. Results of physico-chemical and microbiological investigations showed high ability to reduce Fusarium oxysporum, Alternaria alternata, Aspergillus niger and Botrytis cinerea growth. The suppressive ability detected using confrontation test and the phytostimulatory effect tested on tomato seeds were related mainly to its microbial population content. Among 150 bacterial strains, isolated from the compost extract, 13 isolates showed antifungal activity against the four tested plant pathogenic fungi. Their identification based on 16S rRNA gene sequence revealed they belonged to different species of the genus Bacillus, Alcaligenes, Providencia and Ochrobactrum. When tested for their ability to produce cell wall degradation enzymes using specific media, the majority of the 13 isolates were shown to synthesize proteases, lipases and glucanases. Similarly, the best part of them showed positive reaction for plant growth promoting substances liberation, biosurfactant production and biofilm formation. In vivo tests were carried out using tomato seeds and fruits and proved that 92% of strains improved tomato plants vigor indexes when compared to the control and 6 among them were able to reduce decay severity caused by B. cinerea over 50%. Principal component analysis showed an important correlation between in vitro and in vivo potentialities and that Bacillus siamensis CEBZ11 strain was statistically the most effective strain in protecting tomato plants from gray mould disease. This study revealed the selected strains would be useful for plant pathogenic fungi control and plant growth promotion.

Diversity of culturable bacteria isolated from ancestral crops of Arica and Parinacota Region, Atacama Desert

Arica and Parinacota Region is located at the extreme north of the Atacama Desert, where the high levels of salts and boron, lack of rain, high UV radiation, among other conditions, make this zone an extreme environment. Despite these characteristics, in the transversal valleys, different types of crops are cultivated in this region, which are associated to beneficial microorganisms with specific traits that allow plants surviving and developing under extreme conditions. However, there is incomplete information related to these microorganisms. In this work, bacteria associated with ancestral crops were isolated from oregano, alfalfa, maize, potato, and grapevine samples from Belén, Codpa, Molinos, Poconchile and Socoroma localities, representing the first report of these microorganisms in those sites. Bacteria were identified, being γ-Proteobacteria, the most frequent class (~ 74.4%), with members of Pseudomonas genus the most common isolated genus. All bacteria were functionally characterized for plant growth-promoting activities, including siderophores and auxins production, phosphate solubilization, and nitrogen fixation, revealing an extraordinary potential from these microorganisms for agricultural applications under arid and semiarid conditions.

Synergic Involvements of Microorganisms in the Biomedical Increase of Polyphenols and Flavonoids during the Fermentation of Ginger Juice

Steered fermentation by microorganisms gives great added value in the nutritional quality of local food. Ginger rhizome naturally contains a myriad of bioactive compounds including polyphenol and flavonoids. The aim of this work was to ferment the ginger juice, to evaluate the biochemical parameters of ginger wine, and to understand the involvement of microorganisms in the bioincrease of polyphenol compounds. Titratable acidity and pH values were determined and showed that pH is around 1.6 at the end of the fermentation when the acidity is around 6.431 g/L. Using colorimetric assay, the total polyphenolic and flavonoid compounds were evaluated throughout the fermentation. The variation of the polyphenol and flavonoid concentrations of the unsweetened sample was around 10.18 to 14.64 mg Eq AG/g and 1.394 to 2.224 mg Eq Cat/g Ms, but those from the sweet sample were around 10.82 to 18.34 mg Eq AG/g Ms and 1.311 to 2.290 mg Eq Cat/g. Using one-step PCR, multiplex techniques with specific primers, with yeast-like phenotype 27.27% (6), have been assigned among 22 isolates to Saccharomyces cerevisiae. By using PCR multiplex techniques, Bacillus licheniformis, Bacillus pumilus, Bacillus safensis, and Saccharomyces cerevisiae have been identified. Together with Saccharomyces cerevisiae, we showed that Bacillus sp. are able to secrete enzymatic landscape with some activities up to 50% including cellulase, amylase, pectinase, and protease.

The Status of Soil Microbiome as Affected by the Application of Phosphorus Biofertilizer: Fertilizer Enriched with Beneficial Bacterial Strains

Regarding the unfavourable changes in agroecosystems resulting from the excessive application of mineral fertilizers, biopreparations containing live microorganisms are gaining increasing attention. We assumed that the application of phosphorus mineral fertilizer enriched with strains of beneficial microorganisms contribute to favourable changes in enzymatic activity and in the genetic and functional diversity of microbial populations inhabiting degraded soils. Therefore, in field experiments conditions, the effects of phosphorus fertilizer enriched with bacterial strains on the status of soil microbiome in two chemically degraded soil types (Brunic Arenosol - BA and Abruptic Luvisol - AL) were investigated. The field experiments included treatments with an optimal dose of phosphorus fertilizer (without microorganisms - FC), optimal dose of phosphorus fertilizer enriched with microorganisms including Paenibacillus polymyxa strain CHT114AB, Bacillus amyloliquefaciens strain AF75BB and Bacillus sp. strain CZP4/4 (FA100) and a dose of phosphorus fertilizer reduced by 40% and enriched with the above-mentioned bacteria (FA60). The analyzes performed included: the determination of the activity of the soil enzymes (protease, urease, acid phosphomonoesterase, β-glucosidase), the assessment of the functional diversity of microorganisms with the application of BIOLOGTM plates and the characterization of the genetic diversity of bacteria, archaea and fungi with multiplex terminal restriction fragment length polymorphism and next generation sequencing. The obtained results indicated that the application of phosphorus fertilizer enriched with microorganisms improved enzymatic activity, and the genetic and functional diversity of the soil microbial communities, however these effects were dependent on the soil type.

Integrated use of phosphate-solubilizing Bacillus subtilis strain IA6 and zinc-solubilizing Bacillus sp. strain IA16: a promising approach for improving cotton growth

Mineral nutrition of crop plants is one of the major challenges faced by modern agriculture, particularly in arid and semi-arid regions. In alkaline calcareous soils, the availability of phosphorus and zinc is critically less due to their fixation and precipitation as complexes. Farmers use fertilizers to fulfill crop requirements, but their efficacy is less, which increases production costs. Plant growth-promoting rhizobacteria (PGPR) can improve the availability of crop nutrients through solubilizing the insoluble compounds of phosphorus and zinc in soil. In the present study, a total of 40 rhizobacterial isolates were isolated from cotton rhizosphere and screened for improving cotton growth through the solubilization of phosphorus and zinc. Out of these 40 isolates, seven isolates (IA2, IA3, IA6, IA7, IA8, IA13, and IA14) efficiently solubilized insoluble rock phosphate while seven isolates (IA10, IA16, IA20, IA23, IA24, IA28, and IA30) were more efficient in solubilizing insoluble zinc oxide. In liquid media, strain IA7 (2.75 μg/mL) solubilized the highest amount of phosphate while the highest concentration of soluble zinc was observed in the broth inoculated with strain IA20 (3.94 μg/mL). Seven phosphate-solubilizing and seven zinc-solubilizing strains were evaluated using jar trial to improve the growth of cotton seedlings, and the results were quite promising. All the inoculated treatments showed improvement in growth parameters in comparison with control. Best results were shown by the combined application of IA6 and IA16, followed by the combination of strains IA7 and IA20. Based on the jar trial, the selected isolates were further characterized by plant growth-promoting characters such as siderophores production, HCN production, ammonia production, and exopolysaccharides production. These strains were identified through 16S rRNA sequencing as Bacillus subtilis IA6 (accession # MN005922), Paenibacillus polymyxa IA7 (accession # MN005923), Bacillus sp. IA16 (accession # MN005924), and Bacillus aryabhattai IA20 (accession # MN005925). It is hence concluded that the integrated use of phosphate-solubilizing and zinc-solubilizing strains as potential inoculants can be a promising approach for improving cotton growth under semi-arid conditions.

Different types of agricultural land use drive distinct soil bacterial communities

Biogeographic patterns in soil bacterial communities and their responses to environmental variables are well established, yet little is known about how different types of agricultural land use affect bacterial communities at large spatial scales. We report the variation in bacterial community structures in greenhouse, orchard, paddy, and upland soils collected from 853 sites across the Republic of Korea using 16S rRNA gene pyrosequencing analysis. Bacterial diversities and community structures were significantly differentiated by agricultural land-use types. Paddy soils, which are intentionally flooded for several months during rice cultivation, had the highest bacterial richness and diversity, with low community variation. Soil chemical properties were dependent on agricultural management practices and correlated with variation in bacterial communities in different types of agricultural land use, while the effects of spatial components were little. Firmicutes, Chloroflexi, and Acidobacteria were enriched in greenhouse, paddy, and orchard soils, respectively. Members of these bacterial phyla are indicator taxa that are relatively abundant in specific agricultural land-use types. A relatively large number of taxa were associated with the microbial network of paddy soils with multiple modules, while the microbial network of orchard and upland soils had fewer taxa with close mutual interactions. These results suggest that anthropogenic agricultural management can create soil disturbances that determine bacterial community structures, specific bacterial taxa, and their relationships with soil chemical parameters. These quantitative changes can be used as potential biological indicators for monitoring the impact of agricultural management on the soil environment.

Study on the Identification Methods for Effective Microorganisms in Commercially Available Organic Agriculture Materials

The identification of microorganisms in closely related groups is challenging. The present work focused on the different molecular methodology for the accurate microbial identification in the five commercially available organic agriculture materials enriched with effective microorganisms. From the tested five organic agricultural materials, a total of seven distinct bacterial colonies (A-1, B-1, C-1, D-1, E-1, E-2, and E-3) were isolated and processed for sequential identification utilizing HiCrome™ Bacillus agar, biochemical tests with API CHB50, 16S rRNA gene analysis, random amplified polymorphic DNA (RAPD), and species-specific PCR analysis. All the isolated microorganisms were Gram-positive rods and spore former belonging to Bacillus group and appeared as a differential characteristic feature on HiCrome™ Bacillus agar. All isolates showed high-percentage similarities with the different members of Bacillus species in biochemical testing and 16S rRNA gene analysis. The collective identification results revealed isolates, A-1, B-1, and C-1, close to B. velezensis. Further RAPD-PCR and species-specific PCR discriminated and provided confirmatory evidence for D-1 as B. thuringiensis and E-1, E-2, and E-3 as B. licheniformis, respectively. In addition, presence of B. thuringiensis was also confirmed by toxin crystal protein staining. In conclusion, the species-specific primers could be used as a rapid and accurate identification tool to discriminate closely related Bacillus species such as B. subtilis, B. licheniformis, and B. thuringiensis.

Trichoderma Enhances Net Photosynthesis, Water Use Efficiency, and Growth of Wheat (Triticum aestivum L.) under Salt Stress

Soil salinity is one of the most important abiotic stresses limiting plant growth and productivity. The breeding of salt-tolerant wheat cultivars has substantially relieved the adverse effects of salt stress. Complementing these cultivars with growth-promoting microbes has the potential to stimulate and further enhance their salt tolerance. In this study, two fungal isolates, Th4 and Th6, and one bacterial isolate, C7, were isolated. The phylogenetic analyses suggested that these isolates were closely related to Trichoderma yunnanense, Trichoderma afroharzianum, and Bacillus licheniformis, respectively. These isolates produced indole-3-acetic acid (IAA) under salt stress (200 mM). The abilities of these isolates to enhance salt tolerance were investigated by seed coatings on salt-sensitive and salt-tolerant wheat cultivars. Salt stress (S), cultivar (C), and microbial treatment (M) significantly affected water use efficiency. The interaction effect of M x S significantly correlated with all photosynthetic parameters investigated. Treatments with Trichoderma isolates enhanced net photosynthesis, water use efficiency and biomass production. Principal component analysis revealed that the influences of microbial isolates on the photosynthetic parameters of the different wheat cultivars differed substantially. This study illustrated that Trichoderma isolates enhance the growth of wheat under salt stress and demonstrated the potential of using these isolates as plant biostimulants.

When Salt Meddles Between Plant, Soil, and Microorganisms

In extreme environments, the relationships between species are often exclusive and based on complex mechanisms. This review aims to give an overview of the microbial ecology of saline soils, but in particular of what is known about the interaction between plants and their soil microbiome, and the mechanisms linked to higher resistance of some plants to harsh saline soil conditions. Agricultural soils affected by salinity is a matter of concern in many countries. Soil salinization is caused by readily soluble salts containing anions like chloride, sulphate and nitrate, as well as sodium and potassium cations. Salinity harms plants because it affects their photosynthesis, respiration, distribution of assimilates and causes wilting, drying, and death of entire organs. Despite these life-unfavorable conditions, saline soils are unique ecological niches inhabited by extremophilic microorganisms that have specific adaptation strategies. Important traits related to the resistance to salinity are also associated with the rhizosphere-microbiota and the endophytic compartments of plants. For some years now, there have been studies dedicated to the isolation and characterization of species of plants' endophytes living in extreme environments. The metabolic and biotechnological potential of some of these microorganisms is promising. However, the selection of microorganisms capable of living in association with host plants and promoting their survival under stressful conditions is only just beginning. Understanding the mechanisms of these processes and the specificity of such interactions will allow us to focus our efforts on species that can potentially be used as beneficial bioinoculants for crops.

Mining the Microbiome of Key Species from African Savanna Woodlands: Potential for Soil Health Improvement and Plant Growth Promotion

(1) Aims: Assessing bacterial diversity and plant-growth-promoting functions in the rhizosphere of the native African trees Colophospermum mopane and Combretum apiculatum in three landscapes of the Limpopo National Park (Mozambique), subjected to two fire regimes. (2) Methods: Bacterial communities were identified through Illumina Miseq sequencing of the 16S rRNA gene amplicons, followed by culture dependent methods to isolate plant growth-promoting bacteria (PGPB). Plant growth-promoting traits of the cultivable bacterial fraction were further analyzed. To screen for the presence of nitrogen-fixing bacteria, the promiscuous tropical legume Vigna unguiculata was used as a trap host. The taxonomy of all purified isolates was genetically verified by 16S rRNA gene Sanger sequencing. (3) Results: Bacterial community results indicated that fire did not drive major changes in bacterial abundance. However, culture-dependent methods allowed the differentiation of bacterial communities between the sampled sites, which were particularly enriched in Proteobacteria with a wide range of plant-beneficial traits, such as plant protection, plant nutrition, and plant growth. Bradyrhizobium was the most frequent symbiotic bacteria trapped in cowpea nodules coexisting with other endophytic bacteria. (4) Conclusion: Although the global analysis did not show significant differences between landscapes or sites with different fire regimes, probably due to the fast recovery of bacterial communities, the isolation of PGPB suggests that the rhizosphere bacteria are driven by the plant species, soil type, and fire regime, and are potentially associated with a wide range of agricultural, environmental, and industrial applications. Thus, the rhizosphere of African savannah ecosystems seems to be an untapped source of bacterial species and strains that should be further exploited for bio-based solutions.

The Significance of Bacillus spp. in Disease Suppression and Growth Promotion of Field and Vegetable Crops

Bacillus spp. produce a variety of compounds involved in the biocontrol of plant pathogens and promotion of plant growth, which makes them potential candidates for most agricultural and biotechnological applications. Bacilli exhibit antagonistic activity by excreting extracellular metabolites such as antibiotics, cell wall hydrolases, and siderophores. Additionally, Bacillus spp. improve plant response to pathogen attack by triggering induced systemic resistance (ISR). Besides being the most promising biocontrol agents, Bacillus spp. promote plant growth via nitrogen fixation, phosphate solubilization, and phytohormone production. Antagonistic and plant growth-promoting strains of Bacillus spp. might be useful in formulating new preparations. Numerous studies of a wide range of plant species revealed a steady increase in the number of Bacillus spp. identified as potential biocontrol agents and plant growth promoters. Among different mechanisms of action, it remains unclear which individual or combined traits could be used as predictors in the selection of the best strains for crop productivity improvement. Due to numerous factors that influence the successful application of Bacillus spp., it is necessary to understand how different strains function in biological control and plant growth promotion, and distinctly define the factors that contribute to their more efficient use in the field.

Bacillus siamensis Reduces Cadmium Accumulation and Improves Growth and Antioxidant Defense System in Two Wheat (Triticum aestivum L.) Varieties

Bioavailability of cadmium (Cd) metal in the soils due to the scarcity of good quality water and industrial waste could be the major limiting factor for the growth and yield of crops. Therefore, there is a need for a prompt solution to the Cd toxicity, to fulfill increasing food demand resulting from growing world population. Today, a variable range of plant growth promoting rhizobacteria (PGPR) is being used at a large scale in agriculture, to reduce the risk of abiotic stresses on plants and increase crop productivity. The objective of this study was to evaluate the efficacy of Bacillus siamensis in relieving the Cd induced damage in two wheat varieties (i.e., NARC-2009 and NARC-2011) grown in Cd spiked soil at different concentrations (0, 20, 30, 50 mg/kg). The plants under Cd stress accumulated more Cd in the roots and shoots, resulting in severe oxidative stress, evident by an increase in malondialdehyde (MDA) content. Moreover, a decrease in cell osmotic status, and alteration in antioxidant enzymes such as superoxide dismutase (SOD), catalase (CAT), and ascorbate peroxidase (APX) were also observed in wheat plants under Cd stress. As a result, the Cd exposed plants showed a reduction in growth, tissue biomass, photosynthetic pigments, membrane stability, total soluble sugars, and amino acids, in comparison to control plants. The extent of damage was observed to be higher with an increase in Cd concentration. However, the inoculation of wheat with B. siamensis improved plant growth, reduced oxidative stress, and enhanced the activities of antioxidant enzymes in both wheat varieties. B. siamensis amendment brought a considerable improvement in every parameter determined with respect to Cd stress. The response of both wheat varieties on exposure to B. siamensis was positively enhanced, whereas NARC-2009 accumulated less Cd compared to NARC-2011, which indicated a higher tolerance to Cd stress mediated by B. siamensis inoculation. Overall, the B. siamensis reduced the Cd toxicity in wheat plants through the augmentation of the antioxidant defense system and sugars production.