Microbial detoxification of dimethoate through mediated hydrolysis by Brucella sp. PS4: molecular profiling and plant growth-promoting traits

Exploring the plant-growth promoting bacterium Herbaspirillum seropedicae as catalyst of microbiome remodeling and metabolic changes in wheat plants

MAIN CONCLUSION

Inoculation with the PGPB Herbaspirillum seropedicae shapes both the structure and putative functions of the wheat microbiome and causes changes in the levels of various plant metabolites described to be involved in plant growth and health. Plant growth promoting bacteria (PGPB) can establish metabolic imprints in their hosts, contributing to the improvement of plant health in different ways. However, while PGPB imprints on plant metabolism have been extensively characterized, much less is known regarding those affecting plant indigenous microbiomes, and hence it remains unknown whether both processes occur simultaneously. In this study, both 16S amplicon and ITS sequencing analyses were carried out to study both the structural as well as the putative functional changes in the seed-borne endophytic microbiome of wheat plants inoculated with the PGPB Herbaspirillum seropedicae strain RAM10. Concomitantly, Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) analyses were used to investigate the alterations in the root metabolome of PGPB-inoculated plants. PGPB inoculation led to marked differences in the composition of the root microbiome, accompanied by the differential enrichment of microorganisms with putative roles in both plant energy and nitrogen metabolism. In addition, metabolome analyses showed that the levels of 16 metabolites belonging to the phenylpropanoid, terpenoid, and unsaturated fatty acid families were significantly altered in PGPB-inoculated plants. These findings shed light on the interplay between PGPB, the plant and its associated microbiome, indicating that PGPB can act as the driving force mediating long-lasting changes in both the plant metabolome and the plant microbiome.

Herbicide-treated soil as a reservoir of beneficial bacteria: microbiome analysis and PGP bioinoculants in maize

BACKGROUND

Herbicides are integral to agricultural weed management but can adversely affect non-target organisms, soil health, and microbiome. We investigated the effects of herbicides on the total soil bacterial community composition using 16S rRNA gene amplicon community profiling. Further, we aimed to identify herbicide-tolerant bacteria with plant growth-promoting (PGP) capabilities as a mitigative strategy for these negative effects, thereby promoting sustainable agricultural practices.

RESULTS

A bacterial community analysis explored the effects of long-term S-metolachlor application on soil bacterial diversity, revealing that the herbicide's impact on microbial communities is less significant than the effects of temporal factors (summer vs. winter) or agricultural practices (continuous maize cultivation vs. maize-winter wheat rotation). Although S-metolachlor did not markedly alter the overall bacteriome structure in our environmental context, the application of enrichment techniques enabled the selection of genera such as Pseudomonas, Serratia, and Brucella, which were rare in metagenome analysis of soil samples. Strain isolation revealed a rich source of herbicide-tolerant PGP bacteria within the culturable microbiome fraction, termed the high herbicide concentration tolerant (HHCT) bacterial culture collection. Within the HHCT collection, we isolated 120 strains that demonstrated significant in vitro PGP and biocontrol potential, and soil quality improvement abilities. The most promising HHCT isolates were combined into three consortia, each exhibiting a comprehensive range of plant-beneficial traits. We evaluated the efficacy and persistence of these multi-strain consortia during 4-week in pot experiments on maize using both agronomic parameters and 16S rRNA gene community analysis assessing early-stage plant development, root colonization, and rhizosphere persistence. Notably, 7 out of 10 inoculated consortia partners successfully established themselves and persisted in the maize root microbiome without significantly altering host root biodiversity. Our results further evidenced that all three consortia positively impacted both seed germination and early-stage plant development, increasing shoot biomass by up to 47%.

CONCLUSIONS

Herbicide-treated soil bacterial community analysis revealed that integrative agricultural practices can suppress the effects of continuous S-metolachlor application on soil microbial diversity and stabilize microbiome fluctuations. The HHCT bacterial collection holds promise as a source of beneficial bacteria that promote plant fitness while maintaining herbicide tolerance.

Insights into the biodegradation of fipronil through soil microcosm-omics analyses of Pseudomonas sp. FIP_ A4

Fipronil, a phenylpyrazole insecticide, is used to kill insects resistant to conventional insecticides. Though its regular and widespread use has substantially reduced agricultural losses, it has also caused its accumulation in various environmental niches. The biodegradation is an effective natural process that helps in reducing the amount of residual insecticides. This study deals with an in-depth investigation of fipronil degradation kinetics and pathways in Pseudomonas sp. FIP_A4 using multi-omics approaches. Soil-microcosm results revealed ∼87% degradation within 40 days. The whole genome of strain FIP_A4 comprises 4.09 Mbp with 64.6% GC content. Cytochrome P450 monooxygenase and enoyl-CoA hydratase-related protein, having 30% identity with dehalogenase detected in the genome, can mediate the initial degradation process. Proteome analysis revealed differential enzyme expression of dioxygenases, decarboxylase, and hydratase responsible for subsequent degradation. Metabolome analysis displayed fipronil metabolites in the presence of the bacterium, supporting the proposed degradation pathway. Molecular docking and dynamic simulation of each identified enzyme in complex with the specific metabolite disclosed adequate binding and high stability in the enzyme-metabolite complex. This study provides in-depth insight into genes and their encoded enzymes involved in the fipronil degradation and formation of different metabolites during pollutant degradation. The outcome of this study can contribute immensely to developing efficient technologies for the bioremediation of fipronil-contaminated soils.

Microbial detoxification of chlorpyrifos, profenofos, monocrotophos, and dimethoate by a multifaceted rhizospheric Bacillus cereus strain PM38 and its potential for the growth promotion in cotton

Bacillus genera, especially among rhizobacteria, are known for their ability to promote plant growth and their effectiveness in alleviating several stress conditions. This study aimed to utilize indigenous Bacillus cereus PM38 to degrade four organophosphate pesticides (OPs) such as chlorpyrifos (CP), profenofos (PF), monocrotophos (MCP), and dimethoate (DMT) to mitigate the adverse effects of these pesticides on cotton crop growth. Strain PM38 exhibited distinct characteristics that set it apart from other Bacillus species. These include the production of extracellular enzymes, hydrogen cyanide, exopolysaccharides, Indol-3-acetic acid (166.8 μg/mL), siderophores (47.3 μg/mL), 1-aminocyclopropane-1-carboxylate deaminase activity (32.4 μg/mL), and phosphorus solubilization (162.9 μg/mL), all observed at higher concentrations. This strain has also shown tolerance to salinity (1200 mM), drought (20% PEG-6000), and copper and cadmium (1200 mg/L). The amplification of multi-stress-responsive genes, such as acdS, ituC, czcD, nifH, sfp, and pqqE, further confirmed the plant growth regulation and abiotic stress tolerance capability in strain PM38. Following the high-performance liquid chromatography (HPLC) analysis, the results showed striking compatibility with the first kinetic model. Strain PM38 efficiently degraded CP (98.4%), PF (99.7%), MCP (100%), and DMT (95.5%) at a concentration of 300 ppm over 48 h at 35 °C under optimum pH conditions, showing high coefficients of determination (R2) of 0.974, 0.967, 0.992, and 0.972, respectively. The Fourier transform infrared spectroscopy (FTIR) analysis and the presence of opd, mpd, and opdA genes in the strain PM38 further supported the potential to degrade OPs. In addition, inoculating cotton seedlings with PM38 improved root length under stressful conditions. Inoculation of strain PM38 reduces stress by minimizing proline, thiobarbituric acid-reactive compounds, and electrolyte leakage. The strain PM38 has the potential to be a good multi-stress-tolerant option for a biological pest control agent capable of improving global food security and managing contaminated sites.

The potential of Hungarian bauxite residue isolates for biotechnological applications

Bauxite residue (red mud) is considered an extremely alkaline and salty environment for the biota. We present the first attempt to isolate, identify and characterise microbes from Hungarian bauxite residues. Four identified bacterial strains belonged to the Bacilli class, one each to the Actinomycetia, Gammaproteobacteria, and Betaproteobacteria classes, and two to the Alphaproteobacteria class. All three identified fungi strains belonged to the Ascomycota division. Most strains tolerated pH 8-10 and salt content at 5-7% NaCl concentration. Alkalihalobacillus pseudofirmus BRHUB7 and Robertmurraya beringensis BRHUB9 can be considered halophilic and alkalitolerant. Priestia aryabhattai BRHUB2, Penicillium chrysogenum BRHUF1 and Aspergillus sp. BRHUF2 are halo- and alkalitolerant strains. Most strains produced siderophores and extracellular polymeric substances, could mobilise phosphorous, and were cellulose degraders. These strains and their enzymes are possible candidates for biotechnological applications in processes requiring extreme conditions, e.g. bioleaching of critical raw materials and rehabilitation of alkaline waste deposits.

Pesticide-tolerant microbial consortia: Potential candidates for remediation/clean-up of pesticide-contaminated agricultural soil

Reclamation of pesticide-polluted lands has long been a difficult endeavour. The use of synthetic pesticides could not be restricted due to rising agricultural demand. Pesticide toxicity has become a pressing agronomic problem due to its adverse impact on agroecosystems, agricultural output, and consequently food security and safety. Among different techniques used for the reclamation of pesticide-polluted sites, microbial bioremediation is an eco-friendly approach, which focuses on the application of resilient plant growth promoting rhizobacteria (PGPR) that may transform or degrade chemical pesticides to innocuous forms. Such pesticide-resilient PGPR has demonstrated favourable effects on soil-plant systems, even in pesticide-contaminated environments, by degrading pesticides, providing macro-and micronutrients, and secreting active but variable secondary metabolites like-phytohormones, siderophores, ACC deaminase, etc. This review critically aims to advance mechanistic understanding related to the reduction of phytotoxicity of pesticides via the use of microbe-mediated remediation techniques leading to crop optimization in pesticide-stressed soils. The literature surveyed and data presented herein are extremely useful, offering agronomists-and crop protectionists microbes-assisted remedial strategies for affordably enhancing crop productivity in pesticide-stressed soils.

Changes in the Endophytic Bacterial Community of Brassica rapa after Application of Systemic Insecticides

Insecticides not only control target pests but also adversely affect non-target communities including humans, animals, and microbial communities in host plants and soils. The effect of insecticides on non-target communities, especially endophytic bacterial communities, remains poorly understood. Two phases of treatments were conducted to compare the trends in endophytic bacterial response after insecticide application. Endophytic bacteria were isolated at 2 and 4 weeks after germination. Most insecticide treatments showed a declining trend in bacterial diversity and abundance, whereas an increasing trend was observed in the control. Therefore, insecticide use negatively affected non-target endophytic bacterial communities. Bacillus spp. was mostly dominant in the early stage in both insecticide treatment and control groups. Nevertheless, in the matured stage, mostly bacteria including Pseudomonas spp., Priestia spp. were dominant in groups treated with high insecticide concentrations. Therefore, plants can regulate and moderate their microbiome during their lifecycle depending on surrounding environmental conditions.

Phyto-microbiome to mitigate abiotic stress in crop plants

Plant-associated microbes include taxonomically diverse communities of bacteria, archaebacteria, fungi, and viruses, which establish integral ecological relationships with the host plant and constitute the phyto-microbiome. The phyto-microbiome not only contributes in normal growth and development of plants but also plays a vital role in the maintenance of plant homeostasis during abiotic stress conditions. Owing to its immense metabolic potential, the phyto-microbiome provides the host plant with the capability to mitigate the abiotic stress through various mechanisms like production of antioxidants, plant growth hormones, bioactive compounds, detoxification of harmful chemicals and toxins, sequestration of reactive oxygen species and other free radicals. A deeper understanding of the structure and functions of the phyto-microbiome and the complex mechanisms of phyto-microbiome mediated abiotic stress mitigation would enable its utilization for abiotic stress alleviation of crop plants and development of stress-resistant crops. This review aims at exploring the potential of phyto-microbiome to alleviate drought, heat, salinity and heavy metal stress in crop plants and finding sustainable solutions to enhance the agricultural productivity. The mechanistic insights into the role of phytomicrobiome in imparting abiotic stress tolerance to plants have been summarized, that would be helpful in the development of novel bioinoculants. The high-throughput modern approaches involving candidate gene identification and target gene modification such as genomics, metagenomics, transcriptomics, metabolomics, and phyto-microbiome based genetic engineering have been discussed in wake of the ever-increasing demand of climate resilient crop plants.

Elucidating molecular characterization of chlorpyrifos and profenofos degrading distinct bacterial strains for enhancing seed germination potential of Gossypium arboreum L

Chlorpyrifos (CP) and profenofos (PF) are organophosphate pesticides (OPs) widely used in agriculture and are noxious to both fauna and flora. The presented work was designed to attenuate the toxicity of both pesticides in the growth parameters of a cotton crop by applying plant growth-promoting rhizobacteria (PGPR), namely Pseudomonas aeruginosa PM36 and Bacillus sp. PM37. The multifarious biological activities of both strains include plant growth-promoting traits, including phosphate solubilization; indole-3-acetic acid (IAA), siderophore, and HCN production; nitrogen fixation; and enzymatic activity such as cellulase, protease, amylase, and catalase. Furthermore, the molecular profiling of multi-stress-responsive genes, including acdS, ituC, czcD, nifH, and sfp, also confirmed the plant growth regulation and abiotic stress tolerance potential of PM36 and PM37. Both strains (PM36 and PM37) revealed 92% and 89% of CP degradation at 50 ppm and 87% and 81% at 150 ppm within 7 days. Simultaneously 94% and 98% PF degradation was observed at 50 ppm and 90% and 92% at 150 ppm within 7 days at 35 °C and pH 7. Biodegradation was analyzed using HPLC and FTIR. The strains exhibited first-order reaction kinetics, indicating their reliance on CP and PF as energy and carbon sources. The presence of opd, mpd, and opdA genes in both strains also supported the CP and PF degradation potential of both strains. Inoculation of strains under normal and OP stress conditions resulted in a significant increase in seed germination, plant biomass, and chlorophyll contents of the cotton seedling. Our findings indicate that the strains PM36 and PM37 have abilities as biodegraders and plant growth promoters, with potential applications in crop sciences and bioremediation studies. These strains could serve as an environmentally friendly, sustainable, and socially acceptable solution to manage OP-contaminated sites.

New opportunities in plant microbiome engineering for increasing agricultural sustainability under stressful conditions

Plant microbiome (or phytomicrobiome) engineering (PME) is an anticipated untapped alternative strategy that could be exploited for plant growth, health and productivity under different environmental conditions. It has been proven that the phytomicrobiome has crucial contributions to plant health, pathogen control and tolerance under drastic environmental (a)biotic constraints. Consistent with plant health and safety, in this article we address the fundamental role of plant microbiome and its insights in plant health and productivity. We also explore the potential of plant microbiome under environmental restrictions and the proposition of improving microbial functions that can be supportive for better plant growth and production. Understanding the crucial role of plant associated microbial communities, we propose how the associated microbial actions could be enhanced to improve plant growth-promoting mechanisms, with a particular emphasis on plant beneficial fungi. Additionally, we suggest the possible plant strategies to adapt to a harsh environment by manipulating plant microbiomes. However, our current understanding of the microbiome is still in its infancy, and the major perturbations, such as anthropocentric actions, are not fully understood. Therefore, this work highlights the importance of manipulating the beneficial plant microbiome to create more sustainable agriculture, particularly under different environmental stressors.

Bacillus mycoides PM35 Reinforces Photosynthetic Efficiency, Antioxidant Defense, Expression of Stress-Responsive Genes, and Ameliorates the Effects of Salinity Stress in Maize

Soil salinity is one of the abiotic constraints that imbalance nutrient acquisition, hampers plant growth, and leads to potential loss in agricultural productivity. Salt-tolerant plant growth-promoting rhizobacteria (PGPR) can alleviate the adverse impacts of salt stress by mediating molecular, biochemical, and physiological status. In the present study, the bacterium Bacillus mycoides PM35 showed resistance up to 3 M NaCl stress and exhibited plant growth-promoting features. Under salinity stress, the halo-tolerant bacterium B. mycoides PM35 showed significant plant growth-promoting traits, such as the production of indole acetic acid, siderophore, ACC deaminase, and exopolysaccharides. Inoculation of B. mycoides PM35 alleviated salt stress in plants and enhanced shoot and root length under salinity stress (0, 300, 600, and 900 mM). The B. mycoides PM35 alleviated salinity stress by enhancing the photosynthetic pigments, carotenoids, radical scavenging capacity, soluble sugars, and protein content in inoculated maize plants compared to non-inoculated plants. In addition, B. mycoides PM35 significantly boosted antioxidant activities, relative water content, flavonoid, phenolic content, and osmolytes while reducing electrolyte leakage, H₂O₂, and MDA in maize compared to control plants. Genes conferring abiotic stress tolerance (CzcD, sfp, and srfAA genes) were amplified in B. mycoides PM35. Moreover, all reactions are accompanied by the upregulation of stress-related genes (APX and SOD). Our study reveals that B. mycoides PM35 is capable of promoting plant growth and increasing agricultural productivity.

PGPR-Mediated Salt Tolerance in Maize by Modulating Plant Physiology, Antioxidant Defense, Compatible Solutes Accumulation and Bio-Surfactant Producing Genes

Salinity stress is a barrier to crop production, quality yield, and sustainable agriculture. The current study investigated the plant growth promotion, biochemical and molecular characterization of bacterial strain Enterobacter cloacae PM23 under salinity stress (i.e., 0, 300, 600, and 900 mM). E. cloacae PM23 showed tolerance of up to 3 M NaCl when subjected to salinity stress. Antibiotic-resistant Iturin C (ItuC) and bio-surfactant-producing genes (sfp and srfAA) were amplified in E. cloacae PM23, indicating its multi-stress resistance potential under biotic and abiotic stresses. Moreover, the upregulation of stress-related genes (APX and SOD) helped to mitigate salinity stress and improved plant growth. Inoculation of E. cloacae PM23 enhanced plant growth, biomass, and photosynthetic pigments under salinity stress. Bacterial strain E. cloacae PM23 showed distinctive salinity tolerance and plant growth-promoting traits such as indole-3-acetic acid (IAA), siderophore, ACC deaminase, and exopolysaccharides production under salinity stress. To alleviate salinity stress, E. cloacae PM23 inoculation enhanced radical scavenging capacity, relative water content, soluble sugars, proteins, total phenolic, and flavonoid content in maize compared to uninoculated (control) plants. Moreover, elevated levels of antioxidant enzymes and osmoprotectants (Free amino acids, glycine betaine, and proline) were noticed in E. cloacae PM23 inoculated plants compared to control plants. The inoculation of E. cloacae PM23 significantly reduced oxidative stress markers under salinity stress. These findings suggest that multi-stress tolerant E. cloacae PM23 could enhance plant growth by mitigating salt stress and provide a baseline and ecofriendly approach to address salinity stress for sustainable agriculture.