Endophyte-assisted phytoremediation: mechanisms and current application strategies for soil mixed pollutants

Endophytic Bacterial Communities Facilitate the Dissipation of Phthalates in Soil and Their Biodegradation in Oryza Sativa L

The role of endophytic bacterial communities in aiding the degradation of organic pollutants like phthalates (PAEs) in soil and in planta, as well as their effects on pollutant accumulation in plants, remains unclear. Herein, microcosm experiments were conducted with rice cultivated in agricultural soil polluted with di(2-ethylhexyl) phthalate (DEHP) and further verified with PAE-degrading endophytic consortia. Soil indigenous microbes, especially PAE-degrading bacteria, significantly contributed to DEHP dissipation in soil and diminished DEHP accumulation in rice. Endophytic bacterial communities participated in DEHP degradation in planta, as validated by efficient DEHP degradation by in vitro culturable endophytic consortia and abundant PAE-degrading genes. The inoculation of PAE-degrading endophytic consortia demonstrated their immigration between soil and roots (especially in low-PAE-accumulating cultivar), which enhanced DEHP degradation in soil and in planta and subsequently reduced rice PAE accumulation. This study underscores the facilitative role of endophytic bacterial communities in PAE degradation and in lowering PAE accumulation in crops.

Plant endophytic bacteria reduce phthalates accumulation in soil-crop-body system: a review

Phthalate esters (PAEs) represent a class of widely utilized plasticizers, resulting in their pervasive presence in soil and agricultural crops, which poses significant risks to human health. This review examines the current state of PAE pollution, the microbial resources available for PAE degradation, and the associated degradation pathways. It highlights the advantages of endophytic bacteria over environmental microorganisms, including the prolonged survival of inoculated strains, in vivo biodegradation of PAEs, and multifunctional capabilities. Furthermore, the mechanisms by which endophytic bacteria mitigate PAE accumulation across the three defense lines (soil, crops, and the human body) are elucidated. The integrated approach of employing both plants and microbial agents for the remediation of PAEs demonstrates considerable potential for ensuring the safety of agricultural products and safeguarding human health. This work offers new insights into addressing the challenges posed by organic pollutant contamination and reducing PAE accumulation in the human body.

Comprehensive analysis of biotransformation pathways and products of chloramphenicol by Raoultella Ornithinolytica CT3: Pathway elucidation and toxicity assessment

Microbial degradation of chloramphenicol (CAP) has become important for reducing the adverse impact of environmental pollution with antibiotics. Although several pathways for CAP degradation have been identified in various bacteria, multiple metabolic pathways and their respective intermediate metabolites within a single strain are rarely reported. Here, Raoultella ornithinolytica CT3 was first isolated from silkworm excrement using CAP as the sole carbon source, and 100 mg/L CAP was almost completely degraded within 48 h. The biodegradation type of CAP followed first-order kinetics. Twenty-two CAP biotransformation products were identified using high-performance liquid chromatography and ultra-high-performance liquid chromatography coupled with high-resolution mass spectrometry. The CAP biotransformation pathways were predicted mainly in the acetylation and auxiliary pathways of propionylation and butyrylation. The toxicity of CAP biotransformation products was evaluated using the ecological structure-activity relationship (ECOSAR) model and biological indicators. The results showed that the toxicity of the intermediate metabolites changed slightly, but the final metabolite was harmless to the environment. Genomic analysis predicted that genes encoding acetyltransferase, amido-linkage hydrolase, nitroreductase, haloacetate dehalogenase, and protocatechuate 3,4-dioxygenase were associated with CAP biodegradation. This study provides new insights into the microbial degradation pathway of CAP and constitutes an ecological safety assessment for CAP-contaminated environments.

How to deal with xenobiotic compounds through environment friendly approach?

Every year, a huge amount of lethal compounds, such as synthetic dyes, pesticides, pharmaceuticals, hydrocarbons, etc. are mass produced worldwide, which negatively affect soil, air, and water quality. At present, pesticides are used very frequently to meet the requirements of modernized agriculture. The Food and Agriculture Organization of the United Nations (FAO) estimates that food production will increase by 80% by 2050 to keep up with the growing population, consequently pesticides will continue to play a role in agriculture. However, improper handling of these highly persistent chemicals leads to pollution of the environment and accumulation in food chain. These effects necessitate the development of technologies to eliminate or degrade these pollutants. Degradation of these compounds by physical and chemical processes is expensive and usually results in secondary compounds with higher toxicity. The biological strategies proposed for the degradation of these compounds are both cost-effective and eco-friendly. Microbes play an imperative role in the degradation of xenobiotic compounds that have toxic effects on the environment. This review on the fate of xenobiotic compounds in the environment presents cutting-edge insights and novel contributions in different fields. Microbial community dynamics in water bodies, genetic modification for enhanced pesticide degradation and the use of fungi for pharmaceutical removal, white-rot fungi's versatile ligninolytic enzymes and biodegradation potential are highlighted. Here we emphasize the factors influencing bioremediation, such as microbial interactions and carbon catabolism repression, along with a nuanced view of challenges and limitations. Overall, this review provides a comprehensive perspective on the bioremediation strategies.

The pesticides carbofuran and picloram alter the diversity and abundance of soil microbial communities

Many countries widely use pesticides to increase crop productivity in agriculture. However, their excessive and indiscriminate use contaminates soil and other environments and affects edaphic microbial communities. We aimed to examine how the pesticides carbofuran and picloram affect the structure and functionality of soil microbiota using cultivation-independent methods. Total DNA was extracted from microcosms (treated or not with pesticides) for amplification and metabarcoding sequencing for bacteria (16S gene) and fungi (28S gene) using Illumina-MiSeq platform. Data analysis resulted in 6,772,547 valid reads from the sequencing, including 3,450,815 amplicon sequences from the V3-V4 regions of the 16S gene and 3,321,732 sequences from the 28S gene. A total of 118 archaea, 6,931 bacteria, and 1,673 fungi taxonomic operating units were annotated with 97% identity in 24 soil samples. The most abundant phyla were Proteobacteria, Actinobacteria, Acidobacteria, Firmicutes, Chloroflexi, Euryarchaeaota, and Ascomycota. The pesticides reduced the diversity and richness and altered the composition of soil microbial communities and the ecological interactions among them. Picloram exerted the strongest influence. Metabarcoding data analysis from soil microorganisms identified metabolic functions involved in resistance and degradation of contaminants, such as glutathione S-transferase. The results provided evidence that carbofuran and picloram shaped the soil microbial community. Future investigations are required to unravel the mechanisms by which soil microorganisms degrade pesticides.

Diversity and Functional Roles of Root-Associated Endophytic Fungi in Two Dominant Pioneer Trees Reclaimed from a Metal Mine Slag Heap in Southwest China

The utilization of fast-growing, economically valuable woody plants with strong stress resistance, such as poplar and willow, to revegetate severely metal-contaminated mine tailings not only offers a productive and profitable use of abandoned polluted soil resources but also facilitates the phytoremediation of these polluted soils. This study examines the diversity and functional roles of endophytic fungi naturally colonizing the roots of an artificially established Populus yunnanensis forest and the naturally reclaimed pioneer species Coriaria sinica on an abandoned tailing dam in southwest China. Culture-independent analyses revealed that the root systems of both plant species were abundantly colonized by arbuscular mycorrhizal fungi and endophytic fungi, forming rich and diverse endophytic fungal communities predominantly represented by the genera Ilyonectria, Tetracladium, Auricularia, and unclassified members of Helotiales. However, the composition of root endophytic fungal communities differed significantly between the two plant species. Using a culture-dependent approach, a total of 192 culturable endophytic fungal strains were isolated from the roots. The dominant genera included Cadophora, Cladosporium, Cyphellophora, and Paraphoma, most of which were previously identified as dark septate endophytes (DSE). Six representative DSE strains were selected for further study, and significant cadmium tolerance and various plant growth-promoting traits were observed, including the solubilization of insoluble inorganic and organic phosphorus, indole-3-acetic acid (IAA) production, and siderophore synthesis. In greenhouse experiments, inoculating two DSE strains mitigated the inhibitory effects of metal-polluted tailing soil on the growth of P. yunnanensis. This was achieved by reducing heavy metal uptake in roots and limiting metal translocation to the above-ground tissues, thereby promoting plant growth and adaptability. Our findings suggest that as plants reclaim metal-polluted tailings, root-associated endophytic fungal communities also undergo natural succession, playing a critical role in enhancing the host plant's tolerance to stress. Therefore, these restored root-associated fungi, particularly DSE, are essential functional components of the root systems in plants used for tailing reclamation.

Full-chain analysis on emerging contaminants in soil: Source, migration and remediation

Emerging contaminants (ECs) are gaining attention due to their prevalence and potential negative impacts on the environment and human health. This paper provides a comprehensive review of the status and trends of soil pollution caused by ECs, focusing on their sources, migration pathways, and environmental implications. Significant ECs, including plastics, synthetic polymers, pharmaceuticals, personal care products, plasticizers, and flame retardants, are identified due to their widespread use and toxicity. Their presence in soil is attributed to agricultural activities, urban waste, and wastewater irrigation. The review explores both horizontal and vertical migration pathways, with factors such as soil type, organic matter content, and moisture levels influencing their distribution. Understanding the behavior of ECs in soil is critical to mitigating their long-term risks and developing effective soil remediation strategies. The paper also examines the advantages and disadvantages of in situ and ex situ treatment approaches for ECs, highlighting optimal physical, chemical, and biological treatment conditions. These findings provide a fundamental basis for addressing the challenges and governance of soil pollution induced by ECs.

Biotransformation characteristics of tetracycline by strain Serratia marcescens MSM2304 and its mechanism evaluation based on products analysis and genomics

Microbial biotransformation is a recommended and reliable method in face of formidable tetracycline (TC) with broad-spectrum antibacterial activity. Herein, comprehensive characteristics of a newfound strain and its molecular mechanism in process of TC bioremediation were involved in this study. Specifically, Serratia marcescens MSM2304 isolated from pig manure sludge grew well in presence of TC and achieved optimal removal efficiency of 61% under conditions of initial TC concentration of 10 mg/L, pH of 7.0, cell inoculation amount of 5%, and tryptone of 10 g/L as additional carbon. The pathways of biotransformation include EPS biosorption, cell surface biosorption and biodegradation, which enzymatic processes of biodegradation were occurred through TC adsorbed by biofilms was firstly broken down by extracellular enzymes and part of TC migrated towards biofilm interior and degraded by intracellular enzymes. Wherein extracellular polysaccharides in extracellular polymeric substances (EPS) from biofilm of strain MSM2304 mainly performed extracellular adsorption, and changes in position and intensity of CO, =CH and C-O-C/C-O of EPS possible further implied TC adsorption by it. Biodegradation accounting for 79.07% played a key role in TC biotransformation and could be fitted well by first-order model that manifesting rapid and thorough removal. Potential biodegradation pathway including demethylation, dihydroxylation, oxygenation, and ring opening possibly involved in TC disposal process of MSM2304, TC-degrading metabolites exhibited lower toxicity to indicator bacteria relative to parent TC. Whole genome sequencing as underlying molecular evidence revealed that TC resistance genes, dehydrogenases-encoding genes, monooxygenase-encoding genes, and methyltransferase-encoding genes of strain MSM2304 were positively related to TC biodegradation. Collectively, these results favored a theoretical evaluation for Serratia marcescens MSM2304 as a promising TC-control agent in environmental bioremediation processes.

Harnessing microbial interactions with rice: Strategies for abiotic stress alleviation in the face of environmental challenges and climate change

Rice, which feeds more than half of the world's population, confronts significant challenges due to environmental and climatic changes. Abiotic stressors such as extreme temperatures, drought, heavy metals, organic pollutants, and salinity disrupt its cellular balance, impair photosynthetic efficiency, and degrade grain quality. Beneficial microorganisms from rice and soil microbiomes have emerged as crucial in enhancing rice's tolerance to these stresses. This review delves into the multifaceted impacts of these abiotic stressors on rice growth, exploring the origins of the interacting microorganisms and the intricate dynamics between rice-associated and soil microbiomes. We highlight their synergistic roles in mitigating rice's abiotic stresses and outline rice's strategies for recruiting these microorganisms under various environmental conditions, including the development of techniques to maximize their benefits. Through an in-depth analysis, we shed light on the multifarious mechanisms through which microorganisms fortify rice resilience, such as modulation of antioxidant enzymes, enhanced nutrient uptake, plant hormone adjustments, exopolysaccharide secretion, and strategic gene expression regulation, emphasizing the objective of leveraging microorganisms to boost rice's stress tolerance. The review also recognizes the growing prominence of microbial inoculants in modern rice cultivation for their eco-friendliness and sustainability. We discuss ongoing efforts to optimize these inoculants, providing insights into the rigorous processes involved in their formulation and strategic deployment. In conclusion, this review emphasizes the importance of microbial interventions in bolstering rice agriculture and ensuring its resilience in the face of rising environmental challenges.

Differential interference of copper with endophytic bacterial inoculation: Atrazine decontamination in Acorus tatarinowii and culture solution

To clarify the interference effects of inorganic ions, Acorus tatarinowii and endophytic bacterium Herbaspirillum huttiense (Hh) were combined to decontaminate atrazine pollution under different copper levels. This study verified inoculation effects and revealed the complicated processes of atrazine transformation in solutions. 35.9% leaf biomass was promoted by Hh inoculation, and the value was lowered to 7.87% by high doses of copper. The changing trend of leaf N, K, and S contents, and tiller numbers were consistent with that of leaf biomass. Hh injection improved atrazine accumulation by 43.5% in roots, and under copper interference, this value lowered to 10.6%. Hh promoted atrazine deethylation in plants, which was copper-dose dependent in different plant organs. In solutions, atrazine was conjugated with small-molecule secretions at m/z 118, detoxicated into 2-hxydroatrazine and 2-hydroxy-4-acetamido-atrazine, then the triazine ring opened. Copper interference had a more significant impact on residual atrazine conversion products than Hh inoculation treatments. Hh treatment promoted the ring-opening degradation of atrazine in water. The addition of high doses of copper ions promoted the oxidative process of atrazine while inhibiting its ring-opening transformation process in water.

Endophytic Bacillus sp. R1 and Its Roles in Assisting Phytoremediation and Alleviating the Toxicity of Aluminum Combined Phenanthrene Contaminations in Brassica napus

The release of organic and inorganic contaminants into soil from industry, agriculture, and urbanization has become a major issue of international concern, particularly the heavy metals such as aluminum (Al) and the chemical phenanthrene (PHE). Due to their potential toxicity and non-biodegrade in the environment, efficient remediation methods are urgently needed. Recently, research has comprehensively discussed using plants and their endophytes in bioremediation efforts. Endophytic Bacillus sp. R1, isolated from Brassica napus permanently contaminated with Al and PHE, has growth-promoting properties and can efficiently detoxify these contaminants. The pot experiment indicated that compared to the Al combined PHE contaminated soil alone treatment, the R1 treatment led to increased Al accumulation in canola roots across different levels of PHE, Al, and combined PHE and Al contamination. However, Al accumulation in canola shoots and seeds remained unchanged for all treatments. Moreover, PHE in canola roots and shoots was decreased by R1 inoculation and thereby reducing 26.12-60.61% PHE translocated into canola seeds. Additionally, R1 inoculation significantly increased the proportion of extractable Al and, decreased the proportion of acid-soluble inorganic Al and humic-acid Al, but did not affect the concentration of organically complexed Al. In summary, endophyte R1 can degrade PHE, improve canola roots' Al uptake by increasing soil available Al, and scavenge the reactive oxygen species through production of antioxidant enzymes to help alleviate the toxicity of canola co-contaminated with aluminum and phenanthrene.

Current Scenario and Future Prospects of Endophytic Microbes: Promising Candidates for Abiotic and Biotic Stress Management for Agricultural and Environmental Sustainability

Globally, substantial research into endophytic microbes is being conducted to increase agricultural and environmental sustainability. Endophytic microbes such as bacteria, actinomycetes, and fungi inhabit ubiquitously within the tissues of all plant species without causing any harm or disease. Endophytes form symbiotic relationships with diverse plant species and can regulate numerous host functions, including resistance to abiotic and biotic stresses, growth and development, and stimulating immune systems. Moreover, plant endophytes play a dominant role in nutrient cycling, biodegradation, and bioremediation, and are widely used in many industries. Endophytes have a stronger predisposition for enhancing mineral and metal solubility by cells through the secretion of organic acids with low molecular weight and metal-specific ligands (such as siderophores) that alter soil pH and boost binding activity. Finally, endophytes synthesize various bioactive compounds with high competence that are promising candidates for new drugs, antibiotics, and medicines. Bioprospecting of endophytic novel secondary metabolites has given momentum to sustainable agriculture for combating environmental stresses. Biotechnological interventions with the aid of endophytes played a pivotal role in crop improvement to mitigate biotic and abiotic stress conditions like drought, salinity, xenobiotic compounds, and heavy metals. Identification of putative genes from endophytes conferring resistance and tolerance to crop diseases, apart from those involved in the accumulation and degradation of contaminants, could open new avenues in agricultural research and development. Furthermore, a detailed molecular and biochemical understanding of endophyte entry and colonization strategy in the host would better help in manipulating crop productivity under changing climatic conditions. Therefore, the present review highlights current research trends based on the SCOPUS database, potential biotechnological interventions of endophytic microorganisms in combating environmental stresses influencing crop productivity, future opportunities of endophytes in improving plant stress tolerance, and their contribution to sustainable remediation of hazardous environmental contaminants.

Control Effect and Mechanism of Trichoderma asperellum TM11 against Blueberry Root Rot

Fusarium oxysporum is the primary pathogen of blueberry root rot; furthermore, we found that Fusarium commune can also cause root rot in blueberries. Trichoderma spp. is widely used to control plant diseases. We isolated Trichoderma asperellum (TM11) from blueberry rhizosphere soil to explore its control effect and mechanism on F. oxysporum and F. commune. We found that the inhibitory effects of TM11 volatiles and broth metabolites on F. oxysporum were significant, but only F. commune volatile metabolites had a significant inhibitory effect on its growth. Twelve known antimicrobial metabolites were detected from the methanol extract of TM11 fermentation broth by HPLC-MS. TM11 lysed and coiled around the hyphae of F. oxysporum and F. commune. The pot experiment showed that TM11 had significant control effects against F. oxysporum and F. commune, and inoculation of TM11 prior to that of F. oxysporum and F. commune was more effective. The TM11, TM11 and F. oxysporum, or F. commune and distilled water treatments had different effects on the activities of superoxide dismutase, peroxidase and catalase, and the enzyme activity levels exhibited the following order: TM11 > TM11 and F. oxysporum or F. commune > distilled water. The results showed that TM11 provided effective control of blueberry root rot.

Biochar applications for treating potentially toxic elements (PTEs) contaminated soils and water: a review

Environmental pollution with potentially toxic elements (PTEs) has become one of the critical and pressing issues worldwide. Although these pollutants occur naturally in the environment, their concentrations are continuously increasing, probably as a consequence of anthropic activities. They are very toxic even at very low concentrations and hence cause undesirable ecological impacts. Thus, the cleanup of polluted soils and water has become an obligation to ensure the safe handling of the available natural resources. Several remediation technologies can be followed to attain successful remediation, i.e., chemical, physical, and biological procedures; yet many of these techniques are expensive and/or may have negative impacts on the surroundings. Recycling agricultural wastes still represents the most promising economical, safe, and successful approach to achieving a healthy and sustainable environment. Briefly, biochar acts as an efficient biosorbent for many PTEs in soils and waters. Furthermore, biochar can considerably reduce concentrations of herbicides in solutions. This review article explains the main reasons for the increasing levels of potentially toxic elements in the environment and their negative impacts on the ecosystem. Moreover, it briefly describes the advantages and disadvantages of using conventional methods for soil and water remediation then clarifies the reasons for using biochar in the clean-up practice of polluted soils and waters, either solely or in combination with other methods such as phytoremediation and soil washing technologies to attain more efficient remediation protocols for the removal of some PTEs, e.g., Cr and As from soils and water.

Bacterial Communities Associated with the Roots of Typha spp. and Its Relationship in Phytoremediation Processes

Heavy metal pollution is a severe concern worldwide, owing to its harmful effects on ecosystems. Phytoremediation has been applied to remove heavy metals from water, soils, and sediments by using plants and associated microorganisms to restore contaminated sites. The Typha genus is one of the most important genera used in phytoremediation strategies because of its rapid growth rate, high biomass production, and the accumulation of heavy metals in its roots. Plant growth-promoting rhizobacteria have attracted much attention because they exert biochemical activities that improve plant growth, tolerance, and the accumulation of heavy metals in plant tissues. Because of their beneficial effects on plants, some studies have identified bacterial communities associated with the roots of Typha species growing in the presence of heavy metals. This review describes in detail the phytoremediation process and highlights the application of Typha species. Then, it describes bacterial communities associated with roots of Typha growing in natural ecosystems and wetlands contaminated with heavy metals. Data indicated that bacteria from the phylum Proteobacteria are the primary colonizers of the rhizosphere and root-endosphere of Typha species growing in contaminated and non-contaminated environments. Proteobacteria include bacteria that can grow in different environments due to their ability to use various carbon sources. Some bacterial species exert biochemical activities that contribute to plant growth and tolerance to heavy metals and enhance phytoremediation.

Enhanced mercury phytoremediation by Pseudomonodictys pantanalensis sp. nov. A73 and Westerdykella aquatica P71

Mercury is a non-essential and toxic metal that induces toxicity in most organisms, but endophytic fungi can develop survival strategies to tolerate and respond to metal contaminants and other environmental stressors. The present study demonstrated the potential of mercury-resistant endophytic fungi in phytoremediation. We examined the functional traits involved in plant growth promotion, phytotoxicity mitigation, and mercury phytoremediation in seven fungi strains. The endophytic isolates synthesized the phytohormone indole-3-acetic acid, secreted siderophores, and solubilized phosphate in vitro. Inoculation of maize (Zea mays) plants with endophytes increased plant growth attributes by up to 76.25%. The endophytic fungi stimulated mercury uptake from the substrate and promoted its accumulation in plant tissues (t test, p < 0.05), preferentially in the roots, which thereby mitigated the impacts of metal phytotoxicity. Westerdykella aquatica P71 and the newly identified species Pseudomonodictys pantanalensis nov. A73 were the isolates that presented the best phytoremediation potential. Assembling and annotation of P. pantanalensis A73 and W. aquatica P71 genomes resulted in genome sizes of 45.7 and 31.8 Mb that encoded 17,774 and 11,240 protein-coding genes, respectively. Some clusters of genes detected were involved in the synthesis of secondary metabolites such as dimethylcoprogen (NRPS) and melanin (T1PKS), which are metal chelators with antioxidant activity; mercury resistance (merA and merR1); oxidative stress (PRX1 and TRX1); and plant growth promotion (trpS and iscU). Therefore, both fungi species are potential tools for the bioremediation of mercury-contaminated soils due to their ability to reduce phytotoxicity and assist phytoremediation.

Effect of Arsenic on EPS Synthesis, Biofilm Formation, and Plant Growth-Promoting Abilities of the Endophytes Pseudomonas PD9R and Rahnella laticis PD12R

Phytoremediation, a cost-effective, eco-friendly alternative to conventional remediation, could expand efforts to remediate arsenic-contaminated soils. As with other pollutants, the plant microbiome may improve phytoremediation outcomes for arsenic-contaminated sites. We used in vitro and in silico methods to compare the arsenic resistance mechanisms, synthesis of extracellular polymeric substances (EPS), biofilm formation, and plant growth-promoting abilities of the endophytes Pseudomonas sp. PD9R and Rahnella laticis PD12R. PD12R, which tolerates arsenate (As(V)) and arsenite (As(III)) to concentrations fivefold greater than PD9R, synthesizes high volumes of EPS in response to arsenic, and sequesters arsenic in the capsular EPS and cells. While arsenic exposure induced EPS synthesis in both strains, only PD12R continued to form biofilms at high As(III) and As(V) concentrations. The effects of endophyte inoculation on Arabidopsis growth varied by strain and As(V) concentration, and PD9R had positive effect on plants exposed to low levels of arsenic. Comparative genomic analyses exploring the EPS synthesis and arsenic resistance mechanisms against other Pseudomonas and Rahnella strains suggest that both strains possess atypical arsenic resistance mechanisms from other plant-associated strains, while the configuration of the EPS synthesis systems appeared to be more broadly distributed among plant- and non-plant-associated strains.

Impact of Iron Mining Activity on the Endophytic Fungal Community of Aspilia grazielae

Aspilia grazielae (J. U. Santos) is an endemic plant species in Morro do Urucum in the Pantanal wetland (Brazil). A. grazielae is used for the restoration of areas impacted by iron mining activities. This study evaluates the diversity (composition, value and abundance) of endophytic fungal communities, considering parts of the plant and soil condition. The leaves and roots of A. grazielae were collected from native vegetation areas (NVA) and recovery areas (RCA) in Morro do Urucum. Illumina sequencing technology was used to investigate variation in endophytic fungal biodiversity. The operational taxonomic units detected in NVA ranged from 183 to 263 (leaf) and 115 to 285 (root), while RCA samples ranged from 200 to 282 (leaf) and 156 to 348 (root). Ascomycota phylum was the most common species among all plant samples. The most significant classes identified were Lecanoromycetes and Dothideomycetes that differed significantly (p ≤ 0.05) according to their plant hosts and soil stress. The relative abundance of Pestalotiopsis (Sordariomycetes class) and Stereocaulon (Lecanoromycetes class) genera was influenced by the iron mining activities according to the leaf samples analysed. However, the abundance and wealth of endophytic fungal communities in A. grazielae from RCA were evidence that could explain their high resilience to environmental disturbances and the source-sink dynamics of fungal propagules.

Meta-analytic evidence that allelopathy may increase the success and impact of invasive grasses

Background

In the grass family, a disproportionate number of species have been designated as being invasive. Various growth traits have been proposed to explain the invasiveness of grasses; however, the possibility that allelopathy gives invasive grasses a competitive advantage has attracted relatively little attention. Recent research has isolated plant allelochemicals that are mostly specific to the grass family that can breakdown into relatively stable, toxic byproducts.

Methods

We conducted a meta-analysis of studies on grass allelopathy to test three prominent hypotheses from invasion biology and competition theory: (1) on native recipients, non-native grasses will have a significantly more negative effect compared to native grasses (Novel Weapons Hypothesis); (2) among native grasses, their effect on non-native recipients will be significantly more negative compared to their effect on native recipients (Biotic Resistance Hypothesis); and (3) allelopathic impacts will increase with phylogenetic distance (Phylogenetic Distance Hypothesis). From 23 studies, we gathered a dataset of 524 observed effect sizes (delta log response ratios) measuring the allelopathic impact of grasses on growth and germination of recipient species, and we used non-linear mixed-effects Bayesian modeling to test the hypotheses.

Results

We found support for the Novel Weapons Hypothesis: on native recipients, non-native grasses were twice as suppressive as native grasses (22% vs 11%, respectively). The Phylogenetic Distance Hypothesis was supported by our finding of a significant correlation between phylogenetic distance and allelopathic impact. The Biotic Resistance Hypothesis was not supported. Overall, this meta-analysis adds to the evidence that allelochemicals may commonly contribute to successful or high impact invasions in the grass family. Increased awareness of the role of allelopathy in soil legacy effects associated with grass invasions may improve restoration outcomes through implementation of allelopathy-informed restoration practices. Examples of allelopathy-informed practices, and the knowledge needed to utilize them effectively, are discussed, including the use of activated carbon to neutralize allelochemicals and modify the soil microbial community.

Vanadium-resistant endophytes modulate multiple strategies to facilitate vanadium detoxification and phytoremediation in Pteris vittata

Vanadium (V) contamination of soils poses potential risks to humans and ecosystems. This study was conducted to evaluate the effects of endophyte-assisted phytoremediation and to determine the mechanisms involved in V detoxification and plant growth promotion. Results showed that the endophytic bacterium Serratia marcescens PRE01 could successfully colonize the roots and increase the total V uptake of Pteris vittata by 25.4 %, with higher plant biomass and V accumulation in roots. Endophyte inoculation significantly improved the secretion of phytic, malic, and oxalic acids and accelerated FeVO₄ dissolution and subsequent Fe and V uptake in the rhizosphere. Under V stress without inoculation, V removed by shoot uptake, root uptake, and root surface adsorption accounted for 21.76 %, 42.14 %, and 30.93 % of the total V removal efficiency, respectively. To detoxify excess V, PRE01 effectively strengthened the adsorption of V on the root surface, with an increase in its contribution to the total V removal efficiency from 30.93 % to 38.10 %. Furthermore, beneficial endophytes could alleviate oxidative damage caused by V stress by reinforcing the plant antioxidant system and promoting V(V) reduction in root tissues. These findings clearly reveal that inoculation with endophytes is a promising method for modulating multiple strategies to enhance the phytoremediation of V-contaminated soils.

Basic principles for biosurfactant-assisted (bio)remediation of soils contaminated by heavy metals and petroleum hydrocarbons - A critical evaluation of the performance of rhamnolipids

Despite the fact that rhamnolipids are among the most studied biosurfactants, there are still several gaps which must be filled. The aim of this review is to emphasize and to indicate which issues should be taken into account in order to achieve efficient rhamnolipids-assisted biodegradation or phytoextraction of soils contaminated by heavy metals and petroleum hydrocarbons without harmful side effects. Four main topics have been elucidated in the review: effective concentration of rhamnolipids in soil, their potential phytotoxicity, susceptibility to biodegradation and interaction with soil microorganisms. The discussed elements are often closely associated and often overlap, thus making the interpretation of research results all the more challenging. Each dedicated section of this review includes a description of potential issues and questions, an explanation of the background and rationale for each problem, analysis of relevant literature reports and a short summary with possible application guidelines. The main conclusion is that there is a necessity to establish regulations regarding effective concentrations for rhamnolipids-assisted remediation of soil. The use of an improper concentration is the direct cause of all the other discussed phenomena.

Effects of the dual inoculation of dark septate endophytes and Trichoderma koningiopsis on blueberry growth and rhizosphere soil microorganisms

Blueberry is a shallow root plant in which the absorption of nutrients is inefficient, resulting in slow growth under artificial cultivation conditions. Endophytes play an important role in promoting plant growth; however, the effects of Trichoderma spp. and dark septate endophytes (DSEs) on host plant growth and soil microorganisms are still debatable. We isolated two endophytic fungal species, Trichoderma koningiopsis (TK) and a DSE (Amesia nigricolor; AN), from blueberry roots, which can solubilize insoluble phosphorus and produce amylase and cellulase to promote plant growth. We found that under dual inoculation, the colonization rate and colonization intensity of TK were higher than they were under single inoculation with TK, while the colonization rate and colonization intensity of AN were lower under dual inoculation than under single inoculation with AN. The plant nutrients, root activity, available potassium, and parts of soil phosphatase activities were highest under dual inoculation. TK inoculation resulted in the highest diversity and richness in the soil fungi and bacteria, followed by dual inoculation. The abundance of Ascomycota, Acidobacteriae, Firmicutes, and Actinobacteriota increased significantly, resulting in Trichoderma and Vicinamibacteria inoculated with TK, Chaetomium and Alicyclobacillales inoculated with AN, and Hypocreales and Burkholderiaceae with dual inoculation enriched in the soil.

Microplastic pollution in soils, plants, and animals: A review of distributions, effects and potential mechanisms

Increasing production of synthetic plastics and poor management of plastic wastes have dramatically increased the amount of plastics in the environment. In 2014, at the first United Nations Environment Assembly, marine plastic waste pollution was listed as one of the 10 most pressing environmental issues. In addition, there is much plastic waste in terrestrial ecosystems due to substantial residues from agricultural mulching and packing. As a recently recognized pollutant, microplastics (MPs) have attracted significant attention from the public and various governments. Concentrations of MPs in the environment vary among locations, from <100 to >1 × 10⁶ particles per cubic meter. Many studies have addressed the impacts and potential mechanisms of MPs on the environment and organisms. Humans and other organisms can ingest or carry MPs in a variety of passive ways and these MPs can have a range of negative effects on metabolism, function, and health. Additionally, given their large surface area, MPs can sorb various pollutants, including heavy metals and persistent organic pollutants, with serious implications for animals and human wellbeing. However, due to their complexity and a lack of accurate determination methods, the systematic impacts of MP pollution on whole foodwebs are not clearly established. Therefore, this review summarizes current research advances in MP pollution, particularly the impact of MPs on soils, plants, and animals, and proposes potential future research prospects to better characterize MPs.

Parthenium hysterophorus's Endophytes: The Second Layer of Defense against Biotic and Abiotic Stresses

Parthenium hysterophorus L. is considered an obnoxious weed due to its rapid dispersal, fast multiplications, and agricultural and health hazards. In addition to its physio-molecular and phytotoxic allelochemical usage, this weed most probably uses endophytic flora as an additional line of defense to deal with stressful conditions and tolerate both biotic and abiotic stresses. The aim of this article is to report the diversity of endophytic flora (fungi and bacteria) in P. hysterophorus and their role in the stress mitigation (biotic and abiotic) of other important crops. Various endophytes were reported from P.&nbsp;hysterophorus and their roles in crops evaluated under biotic and abiotic stressed conditions. These endophytes have the potential to alleviate different stresses by improving crops/plants growth, development, biomass, and photosynthetic and other physiological traits. The beneficial role of the endophytes may be attributed to stress-modulating enzymes such as the antioxidants SOD, POD and APX and ACC deaminases. Additionally, the higher production of different classes of bioactive secondary metabolites, i.e., flavonoids, proline, and glutathione may also overcome tissue damage to plants under stressed conditions. Interestingly, a number of medicinally important phytochemicals such as anhydropseudo-phlegmcin-9, 10-quinone-3-amino-8-O methyl ether 'anhydropseudophlegmacin-9, 10-quinone-3-amino-8-Omethyl ether were reported from the endophytic flora of P. hysterophorus. Moreover, various reports revealed that fungal and bacterial endophytes of P. hysterophorus enhance plant growth-promoting attributes and could be added to the consortium of biofertilizers.

Engineered bacterium-binding protein promotes root recruitment of functional bacteria for enhanced cadmium removal from wastewater by phytoremediation

Functional bacteria promote the efficiency of phytoremediation by enhancing plant growth and participating in decontamination. However, their activity is frequently compromised by the weakness of their interaction with plant roots. In this study, we designed the artificial protein LcGC composed of a bacterium-binding domain, a GFP fluorescence reporter, and a carbohydrate-binding domain to function as a physical contact between functional bacteria and plant roots. This protein was then expressed in an engineered yeast cell factory and extracted to assess its effect on rhizosphere microbiome composition, plant growth, and cadmium removal in a simulated phytoremediation system containing the remediation plant Lemna minor and the functional heavy metal-capturing bacteria Cupriavidus taiwanensis and Pseudomonas putida. LcGC efficiently bound bacterial cell wall components and glucan, endowing it high efficiency to bind both functional bacteria and plant roots. Scanning microscopy and microbiome analysis revealed that LcGC enhanced root recruitment and colonization of functional bacteria on the root surfaces. Furthermore, LcGC with the aid of single C. taiwanensis or of C. taiwanensis and P. putida in combination promoted plant growth, enhanced tolerance to cadmium-induced oxidative stress, and consequently improved cadmium-removing capacity of the plants, with the percent of cadmium removal reaching up to 91% for LcGC plus C. taiwanensis, and to 96% for LcGC plus C. taiwanensis and P. putida on day 7. This study provided a physical contact-based strategy to enhance the interaction between functional microbes and plant roots for efficient phytoremediation.

3-keto-DON, but Not 3-epi-DON, Retains the in Planta Toxicological Potential after the Enzymatic Biotransformation of Deoxynivalenol

Deoxynivalenol (DON) is a secondary fungal metabolite that is associated with many adverse toxicological effects in agriculture as well as human/animal nutrition. Bioremediation efforts in recent years have led to the discovery of numerous bacterial isolates that can transform DON to less toxic derivatives. Both 3-keto-DON and 3-epi-DON were recently shown to exhibit reduced toxicity, compared to DON, when tested using different cell lines and mammalian models. In the current study, the toxicological assessment of 3-keto-DON and 3-epi-DON using in planta models surprisingly revealed that 3-keto-DON, but not 3-epi-DON, retained its toxicity to a large extent in both duckweeds (Lemna minor L.) and common wheat (Triticum aestivum L.) model systems. RNA-Seq analysis revealed that the exposure of L. minor to 3-keto-DON and DON resulted in substantial transcriptomic changes and similar gene expression profiles, whereas 3-epi-DON did not. These novel findings are pivotal for understanding the environmental burden of the above metabolites as well as informing the development of future transgenic plant applications. Collectively, they emphasize the fundamental need to assess both plant and animal models when evaluating metabolites/host interactions.

Response of Poplar and Associated Fungal Endophytic Communities to a PAH Contamination Gradient

Microbial populations associated to poplar are well described in non-contaminated and metal-contaminated environments but more poorly in the context of polycyclic aromatic hydrocarbon (PAH) contamination. This study aimed to understand how a gradient of phenanthrene (PHE) contamination affects poplar growth and the fungal microbiome in both soil and plant endosphere (roots, stems and leaves). Plant growth and fitness parameters indicated that the growth of Populus canadensis was impaired when PHE concentration increased above 400 mg kg^-1. Values of alpha-diversity indicators of fungal diversity and richness were not affected by the PHE gradient. The PHE contamination had a stronger impact on the fungal community composition in the soil and root compartments compared to that of the aboveground organs. Most of the indicator species whose relative abundance was correlated with PHE contamination decreased along the gradient indicating a toxic effect of PHE on these fungal OTUs (Operational Taxonomic Units). However, the relative abundance of some OTUs such as Cadophora, Alternaria and Aspergillus, potentially linked to PHE degradation or being plant-beneficial taxa, increased along the gradient. Finally, this study allowed a deeper understanding of the dual response of plant and fungal communities in the case of a soil PAH contamination gradient leading to new perspectives on fungal assisted phytoremediation.

Endophytic fungal communities and their biotechnological implications for agro-environmental sustainability

Endophytic fungal communities have attracted a great attention to chemists, ecologists, and microbiologists as a treasure trove of biological resource. Endophytic fungi play incredible roles in the ecosystem including abiotic and biotic stress tolerance, eco-adaptation, enhancing growth and development, and maintaining the health of their host. In recent times, endophytic fungi have drawn a special focus owing to their indispensable diversity, unique distribution, and unparalleled metabolic pathways. The endophytic fungal communities belong to three phyla, namely Mucoromycota, Basidiomycota, and Ascomycota with seven predominant classes Agaricomycetes, Dothideomycetes, Eurotiomycetes, Mortierellomycotina, Mucoromycotina, Saccharomycetes, and Sordariomycetes. In a review of a huge number of research finding, it was found that endophytic fungal communities of genera Aspergillus, Chaetomium, Fusarium, Gaeumannomyces, Metarhizium, Microsphaeropsis, Paecilomyces, Penicillium, Piriformospora, Talaromyces, Trichoderma, Verticillium, and Xylaria have been sorted out and well characterized for diverse biotechnological applications for future development. Furthermore, these communities are remarkable source of novel bioactive compounds with amazing biological activity for use in agriculture, food, and pharmaceutical industry. Endophytes are endowed with a broad range of structurally unique bioactive natural products, including alkaloids, benzopyranones, chinones, flavonoids, phenolic acids, and quinines. Subsequently, there is still an excellent opportunity to explore novel compounds from endophytic fungi among numerous plants inhabiting different niches. Furthermore, high-throughput sequencing could be a tool to study interaction between plants and endophytic fungi which may provide further opportunities to reveal unknown functions of endophytic fungal communities. The present review deals with the biodiversity of endophytic fungal communities and their biotechnological implications for agro-environmental sustainability.

Elaboration of a Phytoremediation Strategy for Successful and Sustainable Rehabilitation of Disturbed and Degraded Land

Humans are dependent upon soil which supplies food, fuel, chemicals, medicine, sequesters pollutants, purifies and conveys water, and supports the built environment. In short, we need soil, but it has little or no need of us. Agriculture, mining, urbanization and other human activities result in temporary land-use and once complete, used and degraded land should be rehabilitated and restored to minimize loss of soil carbon. It is generally accepted that the most effective strategy is phyto-remediation. Typically, phytoremediation involves re-invigoration of soil fertility, physicochemical properties, and its microbiome to facilitate establishment of appropriate climax cover vegetation. A myco-phytoremediation technology called Fungcoal was developed in South Africa to achieve these outcomes for land disturbed by coal mining. Here we outline the contemporary and expanded rationale that underpins Fungcoal, which relies on in situ bio-conversion of carbonaceous waste coal or discard, in order to explore the probable origin of humic substances (HS) and soil organic matter (SOM). To achieve this, microbial processing of low-grade coal and discard, including bio-liquefaction and bio-conversion, is examined in some detail. The significance, origin, structure, and mode of action of coal-derived humics are recounted to emphasize the dynamic equilibrium, that is, humification and the derivation of soil organic matter (SOM). The contribution of plant exudate, extracellular vesicles (EV), extra polymeric substances (EPS), and other small molecules as components of the dynamic equilibrium that sustains SOM is highlighted. Arbuscular mycorrhizal fungi (AMF), saprophytic ectomycorrhizal fungi (EMF), and plant growth promoting rhizobacteria (PGPR) are considered essential microbial biocatalysts that provide mutualistic support to sustain plant growth following soil reclamation and restoration. Finally, we posit that de novo synthesis of SOM is by specialized microbial consortia (or ‘humifiers’) which use molecular components from the root metabolome; and, that combinations of functional biocatalyst act to re-establish and maintain the soil dynamic. It is concluded that a bio-scaffold is necessary for functional phytoremediation including maintenance of the SOM dynamic and overall biogeochemistry of organic carbon in the global ecosystem

Remediation of soils co-contaminated with cadmium and dichlorodiphenyltrichloroethanes by king grass associated with Piriformospora indica: Insights into the regulation of root excretion and reshaping of rhizosphere microbial community structure

Cadmium (Cd) and dichlorodiphenyltrichloroethane (DDT) are frequently detected in agricultural soils, which poses a threat to public health. This study investigated the effects of inoculation of king grass with Piriformospora indica on the remediation of soils co-contaminated with Cd and DDTs. After treatment for 90 days, the dry shoot and root biomass of king grass inoculated with P. indica markedly increased by 13.0-15.8% and 24.1-46.4%, respectively, compared with those of uninoculated plants. Inoculation with P. indica also increased the uptake of Cd and DDTs by shoots and roots of king grass. The removal efficiency of Cd and DDTs from soils reached 4.88-17.4% and 48.4-51.0%, respectively, in the presence of king grass inoculated with P. indica. Under three Cd-DDTs contamination conditions, root secretion of organic acids, alcohol, and polyamines was distinctively stimulated by P. indica inoculation of king grass compared with planting king grass alone. After phytoremediation, changes in soil bacterial and fungal community composition occurred at different contamination levels. Overall, the results showed that king grass associated with P. indica can be adopted for phytoextraction of Cd and DDTs from moderately contaminated soils by regulating root excretion and reshaping rhizosphere microbial community structure.

Biodegradation mechanism of chloramphenicol by Aeromonas media SZW3 and genome analysis

The overuse of chloramphenicol (CAP) due to its low price is detrimental to ecological safety and human health. An earthworm gut content dwelling bacterium, Aeromonas media SZW3, was isolated with capability of CAP biodegradation, and the CAP degradation efficiency reached 55.86% at day 1 and 67.28% at day 6. CAP biodegradation kinetics and characteristic of strain SZW3 determined the factors that affect CAP biodegradation. Thirteen possible biodegradation products were identified, including three novel biodegradation products (CP1, CP2 and CP3), and three potential biodegradation pathway were proposed. Biodegradation reactions include amide bond hydrolysis, nitro group reduction, acetylation, aminoacetylation, dechlorination and oxidation. Genome analysis suggested that the coding gene of RarD (CAP resistance permease), CAP O-acetyltransferase, nitroreductase and haloalkane dehalogenase may be responsible for CAP biodegradation. The proposed complete biodegradation pathway and genome analysis by strain SZW3 provide us new insight of the transformation route and fate of CAP in the environment.

Potentials of Endophytic Fungi in the Biosynthesis of Versatile Secondary Metabolites and Enzymes

World population growth and modernization have engendered multiple environmental problems: the propagation of humans and crop diseases and the development of multi-drug-resistant fungi, bacteria and viruses. Thus, a considerable shift towards eco-friendly products has been seen in medicine, pharmacy, agriculture and several other vital sectors. Nowadays, studies on endophytic fungi and their biotechnological potentials are in high demand due to their substantial, cost-effective and eco-friendly contributions in the discovery of an array of secondary metabolites. For this review, we provide a brief overview of plant–endophytic fungi interactions and we also state the history of the discovery of the untapped potentialities of fungal secondary metabolites. Then, we highlight the huge importance of the discovered metabolites and their versatile applications in several vital fields including medicine, pharmacy, agriculture, industry and bioremediation. We then focus on the challenges and on the possible methods and techniques that can be used to help in the discovery of novel secondary metabolites. The latter range from endophytic selection and culture media optimization to more in-depth strategies such as omics, ribosome engineering and epigenetic remodeling.

Contribution of Piriformospora indica on improving the nutritional quality of greenhouse tomato and its resistance against cu toxicity after humic acid addition to soil

Protected cultivation has a significant contribution in vegetable production. We investigated whether humic acid addition to soil and Piriformospora indica can improve the nutritional quality of greenhouse tomato. We conducted a pot experiment, in which the effects of P. indica inoculation, humic acid addition, and Cu spiking to soil (0, 120, 240, and 500 ppm Cu) were tested. Humic acid addition to soil spiked with 500 ppm Cu decreased the Cu concentration in the fruits of plants inoculated with P. indica from 0.65 to 0.40 mg 100 g Fw^-1, which is still above the maximum allowed limits of Cu in tomato by World Health Organization (WHO). The lycopene and ascorbic acid content of tomato fruits were consistently improved by humic acid addition and P. indica inoculation. The antioxidant enzymes' activity changed in response to humic acid addition, Cu spiking to soil, and P. indica inoculation. With increasing Cu level up to 240 ppm, the activity of superoxide dismutase (SOD) and peroxidase (POD) increased significantly. However, with spiking more Cu to soil, the activity of antioxidant enzymes reduced and the MDA content increased significantly. Addition of humic acid to soil and/or presence of P. indica increased the activity of antioxidant enzymes when the soil spiked with 500 ppm Cu. This study indicated that addition of P. indica and humic acid to the soil can enhance the nutritional quality of greenhouse tomato by reduction of Cu toxicity as a common pollutant in the greenhouse media and increasing the antioxidant content of fruits.

Phenotype Switching in Metal-Tolerant Bacteria Isolated from a Hyperaccumulator Plant

As an adaptation to unfavorable conditions, microorganisms may represent different phenotypes. Azolla filiculoides L. is a hyperaccumulator of pollutants, but the functions of its microbiome have not been well recognized to date. We aimed to reveal the potential of the microbiome for degradation of organic compounds, as well as its potential to promote plant growth in the presence of heavy metals. We applied the Biolog^TM Phenotypic Microarrays platform to study the potential of the microbiome for the degradation of 96 carbon compounds and stress factors and assayed the hydrolytic potential and auxin production by the microorganisms in the presence of Pb, Cd, Cr (VI), Ni, Ag, and Au. We found various phenotype changes depending on the stress factor, suggesting a possible dual function of the studied microorganisms, i.e., in bioremediation and as a biofertilizer for plant growth promotion. Delftia sp., Staphylococcus sp. and Microbacterium sp. exhibited high efficacy in metabolizing organic compounds. Delftia sp., Achromobacter sp. and Agrobacterium sp. were efficient in enzymatic responses and were characterized by metal tolerant. Since each strain exhibited individual phenotype changes due to the studied stresses, they may all be beneficial as both biofertilizers and bioremediation agents, especially when combined in one biopreparation.

Re-vitalizing of endophytic microbes for soil health management and plant protection

Soil health management and increase crop productivity are challenging issues for researchers and scientists. Many research publications have given multiple technological solutions for improving soil health and crop productivity but main problem is sustainability of those technologies under field condition and different agro-climatic zone. Due to the random industrialization, deforestation, mining and other environmental factor reduce soil fertility and human health. Many alternative options e.g., crop rotation, green manuring, integrated farming, biofertilizer (plant-growth-promoting microorganism, microbial consortium of rhizosphere soils), and vermicomposting are available for adapting and improving the soil heath and crop productivity by farmers. Recent trends of new research dimension for sustainable agriculture, endophytic microbes and its consortium is one of the better alternative for increasing crop productivity, soil health and fertility management. However, current trends are focuses on the endophytic microbes, which are present mostly in all plant species. Endophytic microbes are isolated from plant parts-root, shoot, leaf, flower and seeds which have very potential ability of plant growth promotion and bio-controlling agent for enhancing plant growth and development. Mostly plant endophytes showed multi-dimensional (synergistic, mutualistic, symbiotic etc.) interactions within the host plants. It promotes the plant growth, protects from pathogen, and induces resistance against biotic and abiotic environmental stresses, and improves the soil fertility. Till date, most of the scientific research has been done on assuming that interaction of plant endophytes with the host is similar like the plant-growth-promoting microorganism (PGPM). It would be very interesting to explore the functional properties of plant endophytes to modulate the essential gene expression during biotic and abiotic stresses. Endophytes have the ability to induce the soil fertility by improving soil essential nutrient, enzymatic activity and influence the other physiochemical property. In this study, we have discussed details about functional properties of plant endophytes and their mechanism for enhancing plant productivity and soil health and fertility management under climate-resilient agricultural practices. Our main objective is to promote and explore the beneficial plant endophytes for enhancing sustainable agricultural productivity.

The Endophytic Fungus Piriformospora Indica-Assisted Alleviation of Cadmium in Tobacco

Increasing evidence suggests that the endophytic fungus Piriformospora indica helps plants overcome various abiotic stresses, especially heavy metals. However, the mechanism of heavy metal tolerance has not yet been elucidated. Here, the role of P. indica in alleviating cadmium (Cd) toxicities in tobacco was investigated. It was found that P. indica improved Cd tolerance to tobacco, increasing Cd accumulation in roots but decreasing Cd accumulation in leaves. The colonization of P. indica altered the subcellular repartition of Cd, increasing the Cd proportion in cell walls while reducing the Cd proportion in membrane/organelle and soluble fractions. During Cd stress, P. indica significantly enhanced the peroxidase (POD) activity and glutathione (GSH) content in tobacco. The spatial distribution of GSH was further visualized by Raman spectroscopy, showing that GSH was distributed in the cortex of P. indica-inoculated roots while in the epidermis of the control roots. A LC-MS/MS-based label-free quantitative technique evaluated the differential proteomics of P. indica treatment vs. control plants under Cd stress. The expressions of peroxidase, glutathione synthase, and photosynthesis-related proteins were significantly upregulated. This study provided extensive evidence for how P. indica enhances Cd tolerance in tobacco at physiological, cytological, and protein levels.

Rice recruits Sphingomonas strain HJY-rfp via root exudate regulation to increase chlorpyrifos tolerance and boost residual catabolism

Inoculation with pollution-degrading endophytes boosts the catabolism of residual contaminants and promotes the pollution adaptation of host plants. We investigated the interaction pattern between Sphingomonas strain HJY-rfp, a chlorpyrifos-degrading endophytic bacterium, and rice (Oryza sativa) under pesticide stress using hydroponic cultivation. We observed a notable trend of endophytic root colonization in rice plants treated with 10 mg l-1 chlorpyrifos solution, and after 24 h the migration of HJY-rfp enhanced the chlorpyrifos degradation rate in leaves and stems by 53.36% and 40.81%, respectively. Critically, the rice root exudate profile (organic acids and amino acids) changed under chlorpyrifos stress, and variations in the contents of several components affected the chemotactic behaviour of HJY-rfp. HJY-rfp colonization dramatically activated defensive enzymes, which enabled efficient scavenging of reactive oxygen species, and led to 9.8%, 22.5%, and 41.9% increases in shoot length, fresh weight, and accumulation of total chlorophyll, respectively, in rice suffering from oxidative damage by chlorpyrifos. Endophytic colonization caused up-regulation of detoxification genes that have shown a significant positive correlation with chlorpyrifos degradation in vivo. Collectively, our results demonstrate that agrochemical stress causes plants to actively recruit specific symbiotic microbes to detoxify contaminants and survive better under pollution conditions.

Endophytic Fungi-Mediated Biocatalysis and Biotransformations Paving the Way Toward Green Chemistry

Catalysis is a process carried out in the presence of a heterogenous catalyst for accelerating the rate of a chemical reaction. It plays a pivotal role in transition from take, make, and dispose technology to sustainable technology via chemo- and biocatalytic processes. However, chemocatalyzed reactions are usually associated with copious amounts of perilous/hazardous environmental footprints. Therefore, whole-cell biotransformations or enzyme cocktails serve as cleaner biocatalytic alternatives in replacing the classical chemical procedures. These benchmark bioconversion reactions serve as important key technology in achieving the goals of green chemistry by eliminating waste generation at source. For this, nature has always been a driving force in fuelling natural product discovery and related applications. The fungal endophytic community, in particular, has undergone co-evolution with their host plant and has emerged as a powerful tool of genetic diversity. They can serve as a treasure trove of biocatalysts, catalyzing organic transformations of a wide range of substances into enantiopure compounds with biotechnological relevance. Additionally, the biocatalytic potential of endophytic fungi as whole-intact organisms/isolated enzyme systems has been greatly expanded beyond the existing boundaries with the advancement in high-throughput screening, molecular biology techniques, metabolic engineering, and protein engineering. Therefore, the present review illustrates the promising applications of endophytic fungi as biocatalysts for the synthesis of new structural analogs and pharmaceutical intermediates and refinement of existing proteins for novel chemistries.

Constructed wetland, an eco-technology for wastewater treatment: A review on types of wastewater treated and components of the technology (macrophyte, biolfilm and substrate)

Constructed wetland (CW) represents an efficient eco-technological conglomerate interweaving water security, energy possibility and environmental protection. In the context of wastewater treatment technologies requiring substantial efficiency at reduced cost, chemical input and low environmental impact, applications of CW is being demonstrated at laboratory and field level with reasonably high contaminant removal efficiency and ecological benefits. However, along with the scope of applications, role of individual wetland component has to be re-emphasized through related research interventions. Hence, this review distinctively explores the concerns for extracting maximum benefit of macrophyte (focusing on interface of pollutant removal, root radial oxygen loss, root iron plaque, endophyte-macrophyte assisted treatment in CW, and prospects of energy harvesting from macrophyte) and role of biofilm (effect on treatment efficiency, composition and factors affecting) in a CW. Another focus of the review is on recent advances and developments in alternative low-cost substrate materials (including conventional type, industrial by-products, organic waste, mineral based and hybrid type) and their effect on target pollutants. The remainder of this review is organized to discuss the concerns of CW with respect to wastewater type (municipal, industrial, agricultural and farm wastewater). Attempt is made to analyze the practical relevance and significance of these aspects incorporating all recent developments in the areas to help making informed decisions about future directions for research and development related to CW.

Applications of endophytic microbes in agriculture, biotechnology, medicine, and beyond

Endophytes are emerging as integral components of plant microbiomes. Some of them play pivotal roles in plant development and plant responses to pathogens and abiotic stresses, whereas others produce useful and/or interesting secondary metabolites. The appreciation of their abilities to affect plant phenotypes and produce useful compounds via genetic and molecular interactions has paved the way for these abilities to be exploited for health and welfare of plants, humans and ecosystems. Here we comprehensively review current and potential applications of endophytes in the agricultural, pharmaceutical, and industrial sectors. In addition, we briefly discuss the research objectives that should be focused upon in the coming years in order for endophytes and their metabolites to be fully harnessed for potential use in diverse areas.

The plant endosphere world - bacterial life within plants

The plant endosphere is colonized by complex microbial communities and microorganisms, which colonize the plant interior at least part of their lifetime and are termed endophytes. Their functions range from mutualism to pathogenicity. All plant organs and tissues are generally colonized by bacterial endophytes and their diversity and composition depend on the plant, the plant organ and its physiological conditions, the plant growth stage as well as on the environment. Plant-associated microorganisms, and in particular endophytes, have lately received high attention, because of the increasing awareness of the importance of host-associated microbiota for the functioning and performance of their host. Some endophyte functions are known from mostly lab assays, genome prediction and few metagenome analyses; however, we have limited understanding on in planta activities, particularly considering the diversity of micro-environments and the dynamics of conditions. In our review, we present recent findings on endosphere environments, their physiological conditions and endophyte colonization. Furthermore, we discuss microbial functions, the interaction between endophytes and plants as well as methodological limitations of endophyte research. We also provide an outlook on needs of future research to improve our understanding on the role of microbiota colonizing the endosphere on plant traits and ecosystem functioning.

Diversity of bacterial endophyte in Eucalyptus clones and their implications in water stress tolerance

The genus Eucalyptus with over 747 species occurs in wide ecological range and is preferred for bioenergy plantations due to their short rotation, rapid growth and superior wood properties. They are planted in 22 million ha area and India is third largest planter of Eucalyptus. In the present study, the bacterial endophyte community in leaves of six Eucalyptus clones belonging to E. tereticornis and E. camaldulensis was assessed by sequencing the V3-V4 region of the bacterial 16S rRNA gene. The clones were selected based on their response to progressive water stress. A total of 4947 operational taxonomic units (OTUs) were obtained and the dominant phyla were Proteobacteria, Bacteroidetes and Firmicutes. Escherichia coli was enriched in all samples at species level. Comparison of endophyte diversity was conducted between the two species and across the water stress tolerant and susceptible clones. The alpha-diversity analysis revealed that species richness and diversity was high in E. camaldulensis and water stress susceptible clones. LefSe analysis predicted 69 and 54 significantly enriched taxonomic biomarkers between species and stress response groups respectively. A maximum of 49 taxonomic biomarkers were recorded in susceptible group and the significantly enriched species were Bacteroides thetaiotaomicron and Turicibacter sanguinis, while the tolerant group documented 5 biomarkers including oscillibacter sp. The presence of functional biomarkers was also assessed in both the groups. The findings of the present study provides an insight into the diversity of bacterial endophyte in Eucalyptus leaves and to our knowledge this is the first report on documenting the endophyte abundance in water stress responsive Eucalyptus clones.

Patents on Endophytic Fungi for Agriculture and Bio- and Phytoremediation Applications

Plant endophytic fungi spend all or part of their lives inside host tissues without causing disease symptoms. They can colonize the plant to protect against predators, pathogens and abiotic stresses generated by drought, salinity, high concentrations of heavy metals, UV radiation and temperature fluctuations. They can also promote plant growth through the biosynthesis of phytohormones and nutrient acquisition. In recent years, the study of endophytic fungi for biological control of plant diseases and pests has been intensified to try to reduce the ecological and public health impacts due the use of chemicals and the emergence of fungicide resistance. In this review, we examine 185 patents related to endophytic fungi (from January 1988 to December 2019) and discuss their applicability for abiotic stress tolerance and growth promotion of plants, as agents for biocontrol of herbivores and plant pathogens and bio- and phytoremediation applications.

Effect of the freeze-drying process on the phenotypic diversity of Pseudomonas putida strains isolated from the interior of healthy roots of Sida hermaphrodita: Phenotype microarrays (PMs)

The objective of this study was to research the effect of the freeze-drying process on the metabolic changes of Pseudomonas putida strains (E41, E42, R85) isolated from the interior of Sida hermaphrodita roots with the use of the phenotypic microarrays (PM) technology. The proposed method of the freeze-drying process with inulin as component lycoprotectant demonstrated a high bacterial survival ratio (BSR) immediately after freeze-drying and storage after 12 months. While, after 360 days of freeze-drying BSR decreased to value of 74.38. Pseudomonas putida strains were assayed on microplates PM1-PM5, and PM9-PM13 testing 664 different substrates. However, no significant differences in the use of C substrates were observed either before or after the freeze drying process. An insignificant negative effect of the freeze-drying on the use of these substrates was observed. The utilization of N, P and S sources was low or showed no metabolic activity for most of the compounds after freeze-drying. The freeze-drying process increased the sensitivity of the bacteria to antibiotics and selected chemicals. In this study, the freeze-drying process decreased the metabolic activities of the tested strains and their resistance to antibiotics and chemicals.

Azolla filiculoides L. as a source of metal-tolerant microorganisms

The metal hyperaccumulator Azolla filiculoides is accompanied by a microbiome potentially supporting plant during exposition to heavy metals. We hypothesized that the microbiome exposition to selected heavy metals will reveal metal tolerant strains. We used Next Generation Sequencing technique to identify possible metal tolerant strains isolated from the metal-treated plant (Pb, Cd, Cr(VI), Ni, Au, Ag). The main dominants were Cyanobacteria and Proteobacteria constituting together more than 97% of all reads. Metal treatment led to changes in the composition of the microbiome and showed significantly higher richness in the Pb-, Cd- and Cr-treated plant in comparison with other (95–105 versus 36–44). In these treatments the share of subdominant Actinobacteria (0.4–0.8%), Firmicutes (0.5–0.9%) and Bacteroidetes (0.2–0.9%) were higher than in non-treated plant (respectively: 0.02, 0.2 and 0.001%) and Ni-, Au- and Ag-treatments (respectively: <0.4%, <0.2% and up to 0.2%). The exception was Au-treatment displaying the abundance 1.86% of Bacteroidetes. In addition, possible metal tolerant genera, namely: Acinetobacter, Asticcacaulis, Anabaena, Bacillus, Brevundimonas, Burkholderia, Dyella, Methyloversatilis, Rhizobium and Staphylococcus, which form the core microbiome, were recognized by combining their abundance in all samples with literature data. Additionally, the presence of known metal tolerant genera was confirmed: Mucilaginibacter, Pseudomonas, Mycobacterium, Corynebacterium, Stenotrophomonas, Clostridium, Micrococcus, Achromobacter, Geobacter, Flavobacterium, Arthrobacter and Delftia. We have evidenced that A. filiculoides possess a microbiome whose representatives belong to metal-resistant species which makes the fern the source of biotechnologically useful microorganisms for remediation processes.