Sphingomonads in Microbe-Assisted Phytoremediation: Tackling Soil Pollution

Integrative use of biochar and biostimulants improves cadmium detoxification and yield in cotton

Dealing with abiotic stress is a challenge to maintaining sustainable agricultural productivity, especially for the dual stress of soil salinity and heavy metal contamination. A field experiment was conducted in a completely randomized factorial design to assess the combined effects of biochar (BC), plant growth-promoting microorganisms (PGPM), and seaweed extract (SWE) in mitigating cadmium (Cd) toxicity while promoting cotton growth in saline soils. The study included eight treatments: control (CK), single applications of SWE, PGPM, or BC, dual applications of BC + SWE, BC + PGPM, and PGPM + SWE, and a triple application (BC + PGPM + SWE). Results showed that the BC + PGPM + SWE treatment significantly improved soil quality by reducing the Na and Cd bioavailability by 31 % and 34 %, respectively, while enhancing soil organic matter, microbial biomass carbon, and soil enzymatic activity. Antioxidant defense mechanisms in cotton leaves were significantly induced, as indicated by enhanced activity of SOD, APX, DHAR and GR from 1.8-folds in SOD to 3.4-folds the control in GR. Multivariate analysis revealed that enzymatic and non-enzymatic antioxidants of the ascorbate-glutathione cycle seemed to play a key role in oxidative stress mitigation with maintenance of redox homeostasis and chelation of Cd, resulting in a reduction of 18 % and 56 % in Cd translocation factors from root to shoot, and from shoot to bolls, which contributing to a 65 % increase in cotton seed yield. This study demonstrates an integrative approach to enhancing the resilience of the soil and its productivity, thereby offering a scaling-up, eco-friendly strategy toward sustainable agriculture in degraded and stress-prone ecosystems.

Effects of Paenibacillus polymyxa WZ14 inoculation on phytoextraction efficiency and rhizosphere soil bacterial characteristics in multi-heavy metals contaminated soil

Contaminated soils containing multiple heavy metals, including lead (Pb), cadmium (Cd), and copper (Cu), has been identified as the momentous environmental challenge that requires urgent remediation. This study was first used to explore the effects of Paenibacillus polymyxa WZ14 on the phytoremediation of soils co-contaminated with Cd, Pb, and Cu, focusing on heavy metal bioaccumulation, translocation in Sophora xanthantha and Robinia pseudoacacia L., and soil bacterial community structure. The results demonstrated that the WZ14 strain exhibited strong adaptability and growth potential in heavy-metal-contaminated soil, significantly increasing soil organic carbon, hydrolyzed nitrogen, available phosphorus, and available potassium levels, thereby the total biomass of Sophora xanthantha and Robinia pseudoacacia L. significantly increased by 108.50 % and 61.80 %, respectively. Additionally, With the WZ14 treatment, the total accumulation of Cd, Pb and Cu in Sophora xanthantha significantly increased by 121.31 %, 164.56 %, and 110.17 %, respectively, representing the most effective treatment. Pb and Cu accumulation was largely concentrated in the roots, while Cu distribution was relatively uniform across two plants tissues. 16S rRNA analysis identified that Sphingomonas, Flavisolibacter, Bacillus, and Streptomyces as the key bioindicators of heavy metal contamination, and these four species had positive effects confirmed through the Mantel test and LEfSe analysis. Our findings suggest that the WZ14 strain significantly enhances the phytoremediation capacity of Sophora xanthantha in heavy-metal-contaminated soil, highlighting its potential and feasibility of their combined application for restoring soils contaminated with multiple heavy metals.

Responses of natural plastisphere community and zooplankton to microplastic pollution: a review on novel remediation strategies

The ubiquitous presence of microplastics (MP) in different environments has been well documented. Microplastic contamination has rapidly become a serious environmental issue, threatening marine ecosystems and human health. MP has been reported to accumulate organic pollutants associated with various microbial communities. The MP hazard is specifically serious in urban lakes, near-shore beaches, and benthic sediments. To prevent the further spread of MP and mitigate the increasing level of MP contamination, along with its associated environmental and economic concerns, it is essential to address mitigation strategies and their negative impacts. Contributed by low degradability, hydrophobicity, and sorption potential, the plastic surface acts as an important substrate colonized by several microorganisms known as the plastisphere community. Adaptive responses of the plastisphere community, MP ingestion, and surface modifications by the zooplankton provide insight into novel remediation strategies based on integrated natural community-level approaches. Zooplankton studies are extensive and encompass assessments of their abundance, biomass, distribution, and DNA meta-barcoding. Additionally, zooplankton has been utilized as an indicator in various freshwater environmental policies. Overall, employing zooplankton as an indicator in environmental policies is a vital tool for assessing the health of aquatic ecosystems and can assist in guiding management and conservation efforts. This review summarizes (i) the current literature on the estimation of MP distribution in aquatic environments, (ii) the effects of MP accumulation on the environment and its inhabitants, i.e., the interactions with marine microbiota,, (iii) addresses the bioremediation strategies with an emphasis on microbial degradation, ecological functioning and adaptive responses of marine microbes and finally, (iv) the directions of further research aiming to in situ mitigation of MP pollution. Recent advancements have focused on innovative methods such as membrane bioreactors, synthetic biology, organosilane-based techniques, biofilm-mediated remediation, and nanomaterial-enabled strategies. Nano-enabled technologies show substantial potential to enhance microplastic removal efficiency. Further investigation is necessary to develop advanced treatment technologies that can enhance the removal efficiency of microplastics (MPs) in drinking water. Additionally, more research is needed to understand the toxic impacts of MPs on marine ecosystems, including coral reefs, seagrass beds, mangroves, and other important habitats.

Rhizobacteria protective hydrogel to promote plant growth and adaption to acidic soil

Endophytic plant growth promoting rhizobacteria (PGPRs) could replace chemical fertilizers in sustainable agriculture. Unfortunately, they are susceptible to harsh environmental conditions. Here, we proposed a polymeric hydrogel (PMH) consisting of carboxymethyl chitosan, sodium alginate, and calcium chloride for loading and protecting endophytic PGPR. This hydrogel can load endophytic PGPRs to not only boost its growth-promoting efficiency, but also help them adapt more effectively to environments. Using endophytic PGPR Ensifer C5 as model bacteria and Brasscia napus as host, we demonstrate that the PMH facilitate the colonization of endophytic PGPRs in the apical and lateral root primordia regions. Further analysis indicates that the PMH modulate suberin deposition of the endodermal cell layers and regulate the accumulation of auxin at the root tip. Meanwhile, PMH enhances the antioxidant capacity and disease resistance properties of plants by increasing the content of arachidonic acid metabolism intermediates in the plant. Importantly, the combination of PMH and endophytic PGPRs increases the yields of B. napus by approximately 30% in the field. Furthermore, PMH attenuates the loss of endophytic PGPR activity in the acidic environments. Overall, this microbial encapsulation strategy is a promising way to protect fragile endophytic microorganisms, providing attractive avenues in sustainable agriculture.

Phage Cocktail Alleviates Bacterial Canker of Kiwifruit by Modulating Bacterial Community Structure in Field Trial

Bacterial canker of kiwifruit is the most destructive bacterial disease caused by Pseudomonas syringae pv. actinidiae. Bacteriophages are regarded as promising biocontrol agents against kiwifruit bacterial pathogens due to their exceptional host specificity and environmentally friendly nature. However, the underlying mechanism of phages in the control of kiwifruit bacterial canker disease remains elusive. In this study, the field trial results showed that phage cocktail could significantly reduce the incidence of bacterial canker in kiwifruit. The high throughput sequencing results showed that the phage cocktail regulated the impact of pathogen invasion on branch endophytic communities, adjusted the diversity of the bacterial community structure, regulated the composition of rare taxa and abundant taxa, and increased the proportion of deterministic processes in community assembly processes. The phage cocktail significantly reduced the relative abundance of Pseudomonadaceae, Pectobacteriaceae, and Yersiniacea. Furthermore, the application of the phage cocktail resulted in an increase in the relative abundance of Beijerinckiaceae, Sphingomonadaceae, and Xanthomonadaceae, most of which are abundant taxa of the corresponding microbial communities. Additionally, the composition of rare taxa was also altered under the influence of phages. These findings offer perspectives on the phage-mediated biocontrol of kiwifruit bacterial canker and provide practical backing for the implementation of phage cocktails in sustainable agriculture.

Mitigation of thallium threat in paddy soil and rice plant by application of functional biochar

Thallium (Tl) is a highly toxic metal, and its contamination in soils entails high risks to human health via food chain. It remains largely unknown of the effects of applying biochar on Tl uptake in paddy systems despite that few studies have shown that biochar exhibits great potential for decreasing Tl bioavailability in soils. Herein, we examined the mitigating effects of the application of biochar (5 and 20 g/kg pristine biochar; 5 and 20 g/kg Fe/Mn-modified biochar) on Tl uptake in paddy soil and rice plant after an entire rice growth period. The results suggested that the application of Fe/Mn-modified biochar (FMBC) considerably mitigated the accumulation of Tl in different tissues of rice plants. Specifically, total Tl content in rice plants treated with FMBC-20 decreased by over 75% compared with control experiment. In addition, the amendment of FMBC in Tl-rich paddy soils can enhance the communities of microorganisms (Actinobacteria and Proteobacteria). Further analysis of the soil microbial symbiosis network revealed that FMBC promotes the living microorganisms to play modular synergistic interactions, which is crucial for FMBC-induced Tl stabilization in soils. All these findings indicated that FMBC is an efficient and environmentally friendly Tl-immobilization alternative material and can be potentially used in the remediation of Tl-contaminated paddy soils and/or cropland.

Removal of environmental pollutants using biochar: current status and emerging opportunities

In recent times, biochar has emerged as a novel approach for environmental remediation due to its exceptional adsorption capacity, attributed to its porous structure formed by the pyrolysis of biomass at elevated temperatures in oxygen-restricted conditions. This characteristic has driven its widespread use in environmental remediation to remove pollutants. When biochar is introduced into ecosystems, it usually changes the makeup of microbial communities by offering a favorable habitat. Its porous structure creates a protective environment that shields them from external pressures. Consequently, microorganisms adhering to biochar surfaces exhibit increased resilience to environmental conditions, thereby enhancing their capacity to degrade pollutants. During this process, pollutants are broken down into smaller molecules through the collaborative efforts of biochar surface groups and microorganisms. Biochar is also often used in conjunction with composting techniques to enhance compost quality by improving aeration and serving as a carrier for slow-release fertilizers. The utilization of biochar to support sustainable agricultural practices and combat environmental contamination is a prominent area of current research. This study aims to examine the beneficial impacts of biochar application on the absorption and breakdown of contaminants in environmental and agricultural settings, offering insights into its optimization for enhanced efficacy.

Effects of biodegradable (PBAT/PLA) and conventional (LDPE) mulch film residues on bacterial communities and metabolic functions in different agricultural soils

Soil health is a crucial aspect of sustainable agriculture and food production, necessitating attention to the ecological risks associated with substantial amounts of mulch film residues. Biodegradable mulch films (BDMs) carry the same risk of mulch film residues formation as low-density polyethylene (LDPE) mulch films during actual use. More information is needed to elucidate the specific impacts of mulch film residues on the soil environment. Integrated 16S rRNA gene sequencing and non-targeted metabolomics, this study revealed the response patterns of bacterial communities, metabolites, and metabolic functions in the soil from three different agricultural regions to the presence of mulch film residues. LDPE mulch film residues negatively impacted the bacterial communities in the soils of Heilongjiang (HLJ) and Yunnan (YN) and had a lesser impact on the metabolic spectrum in the soils of HLJ, YN, and Xinjiang (XJ). BDM residues had a greater negative impact on all three soils in terms of both the bacterial communities and metabolites. The impact of BDM treatment on the soils of HLJ, YN, and XJ increased sequentially in that order. It is recommended that, when promoting the use of biodegradable mulch films, a fuller assessment should be made, accounting for local soil properties.

Reducing the accumulation of cadmium and phenanthrene in rice by optimizing planting spacing: Role of low-abundance but core rhizobacterial communities

Optimizing planting spacing is a common agricultural practice for enhancing rice growth. However, its effect on the accumulation of cadmium (Cd) and phenanthrene (Phen) in soil-rice systems and the response mechanisms of rhizobacteria to co-contaminants remain unclear. This study found that reducing rice planting spacing to 5 cm and 10 cm significantly decreased the bioavailability of Cd (by 7.9 %-29.5 %) and Phen (by 12.9 %-47.6 %) in the rhizosphere soil by converting them into insoluble forms. The increased accumulation of Cd and Phen in roots and iron plaques (IPs) ultimately led to decreased Cd (by 32.2 %-39.9 %) and Phen (by 4.2 %-17.3 %) levels in brown rice, and also significantly affected the composition of rhizobacteria. Specifically, reducing rice planting spacing increased the abundance of low-abundance but core rhizobacteria in the rhizosphere soil and IPs, including Bacillus, Clostridium, Sphingomonas, Paenibacillus, and Leifsonia. These low-abundance but core rhizobacteria exhibited enhanced metabolic capacities for Cd and Phen, accompanied by increased abundances of Cd-resistance genes (e.g., czcC and czcB) and Phen-degradation genes (e.g., pahE4 and pahE1) within the rhizosphere soil and IPs. Reduced planting spacing had no noticeable impact on rice biomass. These findings provide new insights into the role of low-abundance but core rhizobacterial communities in Cd and Phen uptake by rice, highlighting the potential of reduced planting spacing as an eco-friendly strategy for ensuring the safety of rice production on contaminated paddy soils.

An improved genome editing system for Sphingomonadaceae

The sphingomonads encompass a diverse group of bacteria within the family Sphingomonadaceae, with the presence of sphingolipids on their cell surface instead of lipopolysaccharide as their main common feature. They are particularly interesting for bioremediation purposes due to their ability to degrade or metabolise a variety of recalcitrant organic pollutants. However, research and development on their full bioremediation potential has been hampered because of the limited number of tools available to investigate and modify their genome. Here, we present a markerless genome editing method for Sphingopyxis granuli TFA, which can be further optimised for other sphingomonads. This procedure is based on a double recombination triggered by a DNA double-strand break in the chromosome. The strength of this protocol lies in forcing the second recombination rather than favouring it by pressing a counterselection marker, thus avoiding laborious restreaking or passaging screenings. Additionally, we introduce a modification with respect to the original protocol to increase the efficiency of the screening after the first recombination event. We show this procedure step by step and compare our modified method with respect to the original one by deleting ecfG2, the master regulator of the general stress response in S. granuli TFA. This adds to the genetic tool repertoire that can be applied to sphingomonads and stands as an efficient option for fast genome editing of this bacterial group.

Regulation of quorum sensing activities by the stringent response gene rsh in sphingomonads is species-specific and culture condition dependent

Stringent response and quorum sensing (QS) are two essential mechanisms that control bacterial global metabolism for better survival. Sphingomonads are a clade of bacteria that survive successfully in diverse ecosystems. In silico survey indicated that 36 out of 79 investigated sphingomonads strains contained more than one luxI homolog, the gene responsible for the biosynthesis of QS signal acyl homoserine lactones (AHLs). Investigation of the regulatory effects of the stringent response gene rsh on QS related bioactivities were carried out using rsh mutants of Sphingobium japonicum UT26 and Sphingobium sp. SYK-6, both had three luxI homologs. Results indicated that deletion of rsh upregulated the overall production of AHLs and extracellular polymeric substances (EPS) in both UT26 and SYK-6 in rich medium, but affected expressions of these luxI/luxR homologs in different ways. In the poor medium (1% LB), rsh mutant of SYK-6 significantly lost AHLs production in broth cultivation but not in biofilm cultivation. The regulatory effects of rsh on QS activities were growth phase dependent in UT26 and culture condition dependent in SYK-6. Our results demonstrated the negative regulatory effect of rsh on QS activities in sphingomonads, which were very different from the positive effect found in sphingomonads containing only one luxI/R circuit. This study extends the current knowledge on the intricate networks between stringent response and QS system in sphingomonads, which would help to understand their survival advantage.

Role of biochar pyrolysis temperature on intracellular and extracellular biodegradation of biochar-adsorbed organic compounds

Immobilizing organic pollutants by adsorption of biochar in farmland soil is a cost-effective remediation method for contaminated soil. As the adsorption capacity of biochar is limited, biodegradation of biochar-adsorbed organic pollutants was a potential way to regenerate biochars and maintain the adsorption performance of biochars to lower the cost. It could be affected by the biochar pyrolysis temperature, but was not evaluated yet. In this study, biodegradation of adsorbed phenanthrene on a series of biochars with pyrolysis temperatures from 150 to 700 °C by Sphingobium yanoikuyae B1 was investigated using batch experiments of biodegradation kinetics at 30 °C, to explore the role of biochar pyrolysis temperature on biodegradation of biochar-adsorbed organic compounds. It was observed that 37.5-47.9% of adsorbed phenanthrene on moderate temperature-pyrolyzed biochars produced at 400 and 500 °C were biodegraded, less than that on high temperature-pyrolyzed biochars produced at ≥600 °C (48.8-60.8%) and low temperature-pyrolyzed biochars produced at ≤300 °C (63.4-92.5%). Phenanthrene adsorbed largely on the low temperature-pyrolyzed biochars by partition mechanism and thus is easily desorbed to water for a dominated intracellular biodegradation. On the high temperature-pyrolyzed biochars, phenanthrene is adsorbed largely by pore-filling mechanism and thus less desorbed to water for intracellular biodegradation. However, high temperature-pyrolyzed biochars can promote microbes to produce siderophore, H2O2 and thus release extracellular •OH for a dominated degradation of adsorbed phenanthrene by Fenton-like reaction. With the increase of biochar pyrolysis temperature, desorption and consequently the intracellular biodegradation of adsorbed phenanthrene on biochars decreased, while the secretion of siderophore and H2O2 by microbes on biochars increased to produce more extracellular •OH for degradation by Fenton-like reaction. The results could provide deep insights into the role of biochar pyrolysis temperature on biodegradation of biochar-adsorbed organic compounds, and optimize the selection of biochar with higher adsorption performance and easier regeneration for soil remediation.

Pot experimental trial for assessing the role of different composts on decontamination and reclamation of a polluted soil from an illegal dump site in Southern Italy using Brassica juncea and Sorghum bicolor

A pot experiment was carried out to evaluate the remediation potential of Brassica juncea and Sorghum bicolor in the decontamination of soil polluted with heavy metals such as copper, lead, tin, and zinc along with polychlorinated biphenyls, polycyclic aromatic hydrocarbons, and heavy hydrocarbons. Two composts obtained from different composting processes were tested as biostimulating agents. At the end of the trial, the effect of plant/compost combinations on soil microbial composition, contaminant removal, biochemical indicators, and plant biomass production was determined. The results highlighted that compost addition improved plant biomass despite slowing down plants' removal of organic and inorganic contaminants. In addition, compost partially enhanced the soil biochemical indicators and modified the relative abundance of the rhizosphere microorganisms. Sorghum showed better mitigation performance than Brassica due to its higher growth. The soil fertility level, the choice of plant species, and microbial richness were found fundamental to perform soil remediation. In contrast, compost was relevant for a higher crop biomass yield.

The variations of native plasmids greatly affect the cell surface hydrophobicity of sphingomonads

IMPORTANCE

Microbial cell surface hydrophobicity (CSH) reflects nonspecific adhesion ability and affects various physiological processes, such as biofilm formation and pollutant biodegradation. Understanding the regulation mechanisms of CSH will contribute to illuminating microbial adaptation strategies and provide guidance for controlling CSH artificially to benefit humans. Sphingomonads, a common bacterial group with great xenobiotic-degrading ability, generally show higher CSH than typical Gram-negative bacteria, which plays a positive role in organic pollutant capture and cell colonization. This study verified that the variations of two native plasmids involved in synthesizing outer membrane proteins and polysaccharides greatly affected the CSH of sphingomonads. It is feasible to control their CSH by changing the plasmid copy number and sequences. Additionally, considering that plasmids are likely to evolve faster than chromosomes, the CSH of sphingomonads may evolve quickly to respond to environmental changes. Our results provide valuable insights into the CSH regulation and evolution of sphingomonads.

Reveal molecular mechanism on the effects of silver nanoparticles on nitrogen transformation and related functional microorganisms in an agricultural soil

Silver nanoparticles (AgNPs) are widely present in aquatic and soil environment, raising significant concerns about their impacts on creatures in ecosystem. While the toxicity of AgNPs on microorganisms has been reported, their effects on biogeochemical processes and specific functional microorganisms remain relatively unexplored. In this study, a 28-day microcosmic experiment was conducted to investigate the dose-dependent effects of AgNPs (10 mg and 100 mg Ag kg-1 soil) on nitrogen transformation and functional microorganisms in agricultural soils. The molecular mechanisms were uncovered by examining change in functional microorganisms and metabolic pathways. To enable comparison, the toxicity of positive control with an equivalent Ag+ dose from CH3COOAg was also included. The results indicated that both AgNPs and CH3COOAg enhanced nitrogen fixation and nitrification, corresponding to increased relative abundances of associated functional genes. However, they inhibited denitrification via downregulating nirS, nirK, and nosZ genes as well as reducing nitrate and nitrite reductase activities. In contrast to high dose of AgNPs, low levels increased bacterial diversity. AgNPs and CH3COOAg altered the activities of associated metabolic pathways, resulting in the enrichment of specific taxa that demonstrated tolerance to Ag. At genus level, AgNPs increased the relative abundances of nitrogen-fixing Microvirga and Bacillus by 0.02 %-629.39 % and 14.44 %-30.10 %, respectively, compared with control group (CK). The abundances of denitrifying bacteria, such as Rhodoplanes, Pseudomonas, and Micromonospora, decreased by 19.03 % to 32.55 %, 24.73 % to 50.05 %, and 15.66 % to 76.06 %, respectively, compared to CK. CH3COOAg reduced bacterial network complexity, diminished the symbiosis mode compared to AgNPs. The prediction of genes involved in metabolic pathways related to membrane transporter and cell motility showed sensitive to AgNPs exposure in the soil. Further studies involving metabolomics are necessary to reveal the essential effects of AgNPs and CH3COOAg on biogeochemical cycle of elements in agricultural soil.

Aqueous Organic Hydrogen Gas Proton Batteries with Ultrahigh-Rate and Ultralow-Temperature Performance

Aqueous proton batteries (APBs) have emerged as one of the most promising batteries for large-scale energy storage technology. However, they usually show an undesirable electrochemical performance. Herein, we demonstrate a novel aqueous catalytic hydrogen gas powered organic proton (HOP) battery, which is driven by hydrogen evolution/oxidation redox reactions via commercial nanocatalysts on the anode and coordination/decoordination reactions of C═O with H+ on the cathode. The HOP battery shows an excellent rate capacity of 190.1 mAh g-1 at 1 A g-1 and 71.4 mAh g-1 at 100 A g-1. It also delivers a capacity of 96.6 mAh g-1 after 100000 cycles and operates at temperatures down to -70 °C. Moreover, the HOP battery is fabricated in a large-scale pouch cell with an extended capacity, exhibiting its potential for practical energy storage applications. This work provides new insights into the building of sustainable APBs, which will broaden the horizons of high-performance aqueous batteries.

Hibiscus rosa-sinensis as a potential hyperaccumulator in metal contaminated magnesite mine tailings

Mining is one of the major contributors for land degradation and severe heavy metals based soil pollution. In this study, the physicochemical properties of magnesite mine soil was investigated and assess the optimistic and eco-friendly remediation approach with Hibiscus rosa-sinensis with the effect of pre-isolated Acidithiobacillus thiooxidans. The physicochemical properties analysis results revealed that most the parameter were either too less or beyond the permissible limits. The pre-isolated A. thiooxidans showed remarkable multi-metal tolerance up to 800 μg mL-1 concentration of Cr, Cd, Pb, and Mn. Heavy metal content in polluted soil was reduced to avoid more metal toxicity by diluting with fertile control soil as 80:20 and 60:40. The standard greenhouse experiment was performed to evaluate the phytoextraction potential of H. rosa-sinensis under the influence of A. thiooxidans in various treatment groups (G-I to G-V). The outcome of this investigation was declared that the multi-metal tolerant A. thiooxidans from G-III and G-II showed remarkable effect on growth and phytoextraction ability of H. rosa-sinensis on metal polluted magnesite mine soil in 180 d greenhouse study. These results suggested that the combination of H. rosa-sinensis and A. thiooxidans could be used as an excellent hyper-accumulator to extract metal pollution from polluted soil.

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.

Exploring the Core Bacteria and Functional Traits in Pecan (Carya illinoinensis) Rhizosphere

Pecan (Carya illinoinensis) and Chinese hickory (Carya cathayensis) are important commercially cultivated nut trees. They are phylogenetically closely related plants; however, they exhibit significantly different phenotypes in response to abiotic stress and development. The rhizosphere selects core microorganisms from bulk soil, playing a pivotal role in the plant's resistance to abiotic stress and growth. In this study, we used metagenomic sequencing to compare the selection capabilities of seedling pecan and seedling hickory at taxonomic and functional levels in bulk soil and the rhizosphere. We observed that pecan has a stronger capacity to enrich rhizosphere plant-beneficial microbe bacteria (e.g., Rhizobium, Novosphingobium, Variovorax, Sphingobium, and Sphingomonas) and their associated functional traits than hickory. We also noted that the ABC transporters (e.g., monosaccharide transporter) and bacterial secretion systems (e.g., type IV secretion system) are the core functional traits of pecan rhizosphere bacteria. Rhizobium and Novosphingobium are the main contributors to the core functional traits. These results suggest that monosaccharides may help Rhizobium to efficiently enrich this niche. Novosphingobium may use a type IV secretion system to interact with other bacteria and thereby influence the assembly of pecan rhizosphere microbiomes. Our data provide valuable information to guide core microbial isolation and expand our knowledge of the assembly mechanisms of plant rhizosphere microbes. IMPORTANCE The rhizosphere microbiome has been identified as a fundamental factor in maintaining plant health, helping plants to fight the deleterious effects of diseases and abiotic stresses. However, to date, studies on the nut tree microbiome have been scarce. Here, we observed a significant "rhizosphere effect" on the seedling pecan. We furthermore demonstrated the core rhizosphere microbiome and function in the seedling pecan. Moreover, we deduced possible factors that help the core bacteria, such as Rhizobium, to efficiently enrich the pecan rhizosphere and the importance of the type IV system for the assembly of pecan rhizosphere bacterial communities. Our findings provide information for understanding the mechanism of the rhizosphere microbial community enrichment process.

Microorganisms and Biochar Improve the Remediation Efficiency of Paspalum vaginatum and Pennisetum alopecuroides on Cadmium-Contaminated Soil

Phytoremediation can help remediate potential toxic elements (PTE) in soil. Microorganisms and soil amendments are effective means to improve the efficiency of phytoremediation. This study selected three microorganisms that may promote phytoremediation, including bacteria (Ceratobasidium), fungi (Pseudomonas mendocina), and arbuscular-mycorrhizal fungi (AMF, Funneliformis caledonium). The effects of single or mixed inoculation of three microorganisms on the phytoremediation efficiency of Paspalum vaginatum and Pennisetum alopecuroides were tested under three different degrees of cadmium-contaminated soil (low 10 mg/kg, medium 50 mg/kg, and high 100 mg/kg). The results showed that single inoculation of AMF or Pseudomonas mendocina could significantly increase the biomass of two plants under three different degrees of cadmium-contaminated soil, and the growth-promoting effect of AMF was better than Pseudomonas mendocina. However, simultaneous inoculation of these two microorganisms did not show a better effect than the inoculation of one. Inoculation of Ceratobasidium reduced the biomass of the two plants under high concentrations of cadmium-contaminated soil. Among all treatments, the remediation ability of the two plants was the strongest when inoculated with AMF alone. On this basis, this study explored the effect of AMF combined with corn-straw-biochar on the phytoremediation efficiency of Paspalum vaginatum and Pennisetum alopecuroides. The results showed that biochar could affect plant biomass and Cd concentration in plants by reducing Cd concentration in soil. The combined use of biochar and AMF increased the biomass of Paspalum vaginatum by 8.9-48.6% and the biomass of Pennisetum alopecuroides by 8.04-32.92%. Compared with the single use of AMF or biochar, the combination of the two is better, which greatly improves the efficiency of phytoremediation.

Sulfur fertilization and water management ensure phytoremediation coupled with argo-production by mediating rhizosphere microbiota in the Oryza sativa L.-Sedum alfredii Hance rotation system

Sulfur (S) fertilizers, water management and crop rotation are important agronomic practices, related to soil heavy metal bioavailability. However, the mechanisms of microbial interactions remain unclear. Herein, we investigated how S fertilizers (S⁰ and Na₂SO₄) and water management affected plant growth, soil cadmium (Cd) bioavailability, and rhizospheric bacterial communities in the Oryza sativa L. (rice)-Sedum alfredii Hance (S. alfredii) rotation system through 16S rRNA gene sequencing and ICP-MS analysis. During rice cultivation, continuous flooding (CF) was better than alternating wetting and drying (AWD). CF treatment decreased soil Cd bioavailability by the promotion of insoluble metal sulfide production and soil pH, thus lowering Cd accumulation in grains. S application recruited more S-reducing bacteria in the rhizosphere of rice, whilst Pseudomonas promoted metal sulfide production and rice growth. During S. alfredii cultivation, S fertilizer recruited S-oxidizing and metal-activating bacteria in the rhizosphere. Thiobacillus may oxidize metal sulfides and enhance Cd and S absorption into S. alfredii. Notably, S oxidation decreased soil pH and elevated Cd content, thereby promoting S. alfredii growth and Cd absorption. These findings showed rhizosphere bacteria were involved in Cd uptake and accumulation in the rice-S. alfredii rotation system, thus providing useful information for phytoremediation coupled with argo-production.

Nondesulfurizing benzothiophene biotransformation to hetero and homodimeric ortho-substituted diaryl disulfides by the model PAH-degrading Sphingobium barthaii

Understanding the biotransformation mechanisms of toxic sulfur-containing polycyclic aromatic hydrocarbon (PASH) pollutants such as benzothiophene (BT) is useful for predicting their environmental fates. In the natural environment, nondesulfurizing hydrocarbon-degrading bacteria are major active contributors to PASH biodegradation at petroleum-contaminated sites; however, BT biotransformation pathways by this group of bacteria are less explored when compared to desulfurizing organisms. When a model nondesulfurizing polycyclic aromatic hydrocarbon-degrading soil bacterium, Sphingobium barthaii KK22, was investigated for its ability to cometabolically biotransform BT by quantitative and qualitative methods, BT was depleted from culture media but was biotransformed into mostly high molar mass (HMM) hetero and homodimeric ortho-substituted diaryl disulfides (diaryl disulfanes). HMM diaryl disulfides have not been reported as biotransformation products of BT. Chemical structures were proposed for the diaryl disulfides by comprehensive mass spectrometry analyses of the chromatographically separated products and were supported by the identification of transient upstream BT biotransformation products, which included benzenethiols. Thiophenic acid products were also identified, and pathways that described BT biotransformation and novel HMM diaryl disulfide formation were constructed. This work shows that nondesulfurizing hydrocarbon-degrading organisms produce HMM diaryl disulfides from low molar mass polyaromatic sulfur heterocycles, and this may be taken into consideration when predicting the environmental fates of BT pollutants.

Plant specialized metabolites in the rhizosphere of tomatoes: secretion and effects on microorganisms

Plants interact with microorganisms in the phyllosphere and rhizosphere. Here the roots exude plant specialized metabolites (PSMs) that have diverse biological and ecological functions. Recent reports have shown that these PSMs influence the rhizosphere microbiome, which is essential for the plant's growth and health. This review summarizes several specialized metabolites secreted into the rhizosphere of the tomato plant (Solanum lycopersicum), which is an important model species for plant research and a commercial crop. In this review, we focused on the effects of such plant metabolites on plant-microbe interactions. We also reviewed recent studies on improving the growth of tomatoes by analyzing and reconstructing the rhizosphere microbiome and discussed the challenges to be addressed in establishing sustainable agriculture.

Integrating Biochar, Bacteria, and Plants for Sustainable Remediation of Soils Contaminated with Organic Pollutants

The contamination of soil with organic pollutants has been accelerated by agricultural and industrial development and poses a major threat to global ecosystems and human health. Various chemical and physical techniques have been developed to remediate soils contaminated with organic pollutants, but challenges related to cost, efficacy, and toxic byproducts often limit their sustainability. Fortunately, phytoremediation, achieved through the use of plants and associated microbiomes, has shown great promise for tackling environmental pollution; this technology has been tested both in the laboratory and in the field. Plant-microbe interactions further promote the efficacy of phytoremediation, with plant growth-promoting bacteria (PGPB) often used to assist the remediation of organic pollutants. However, the efficiency of microbe-assisted phytoremediation can be impeded by (i) high concentrations of secondary toxins, (ii) the absence of a suitable sink for these toxins, (iii) nutrient limitations, (iv) the lack of continued release of microbial inocula, and (v) the lack of shelter or porous habitats for planktonic organisms. In this regard, biochar affords unparalleled positive attributes that make it a suitable bacterial carrier and soil health enhancer. We propose that several barriers can be overcome by integrating plants, PGPB, and biochar for the remediation of organic pollutants in soil. Here, we explore the mechanisms by which biochar and PGPB can assist plants in the remediation of organic pollutants in soils, and thereby improve soil health. We analyze the cost-effectiveness, feasibility, life cycle, and practicality of this integration for sustainable restoration and management of soil.

A short exposure to a semi-natural habitat alleviates the honey bee hive microbial imbalance caused by agricultural stress

Honeybee health and the species' gut microbiota are interconnected. Also noteworthy are the multiple niches present within hives, each with distinct microbiotas and all coexisting, which we termed "apibiome". External stressors (e.g. anthropization) can compromise microbial balance and bee resilience. We hypothesised that (1) the bacterial communities of hives located in areas with different degrees of anthropization differ in composition, and (2) due to interactions between the multiple microbiomes within the apibiome, changes in the community of a niche would impact the bacteria present in other hive sections. We characterised the bacterial consortia of different niches (bee gut, bee bread, hive entrance and internal hive air) of 43 hives from 3 different environments (agricultural, semi-natural and natural) through 16S rRNA amplicon sequencing. Agricultural samples presented lower community evenness, depletion of beneficial bacteria, and increased recruitment of stress related pathways (predicted via PICRUSt2). The taxonomic and functional composition of gut and hive entrance followed an environmental gradient. Arsenophonus emerged as a possible indicator of anthropization, gradually decreasing in abundance from agriculture to the natural environment in multiple niches. Importantly, after 16 days of exposure to a semi-natural landscape hives showed intermediate profiles, suggesting alleviation of microbial dysbiosis through reduction of anthropization.

Engineering microbes for enhancing the degradation of environmental pollutants: A detailed review on synthetic biology

Anthropogenic activities resulted in the deposition of huge quantities of contaminants such as heavy metals, dyes, hydrocarbons, etc into an ecosystem. The serious ill effects caused by these pollutants to all living organisms forced in advancement of technology for degrading or removing these pollutants. This degrading activity is mostly depending on microorganisms owing to their ability to survive in harsh adverse conditions. Though native strains possess the capability to degrade these pollutants the development of genetic engineering and molecular biology resulted in engineering approaches that enhanced the efficiency of microbes in degrading pollutants at faster rate. Many bioinformatics tools have been developed for altering/modifying genetic content in microbes to increase their degrading potency. This review provides a detailed note on engineered microbes - their significant importance in degrading environmental contaminants and the approaches utilized for modifying microbes. The genes responsible for degrading the pollutants have been identified and modified fir increasing the potential for quick degradation. The methods for increasing the tolerance in engineered microbes have also been discussed. Thus engineered microbes prove to be effective alternate compared to native strains for degrading pollutants.

Isolation, characterization and application of the epoxiconazole-degrading strain Pseudomonas sp. F1 in a soil-vegetable system

Epoxiconazole (EPX) has a long half-life in soil and causes various toxicological effects in both the ecosystem and mammals. In this study, eight strains of bacteria capable of degrading EPX were isolated from pesticide-contaminated soil, with strain F1 showing the best effect. This strain was identified as Pseudomonas sp. by 16S rRNA gene sequencing and physiological-biochemical analyses. Our results indicated that strain F1 has a high capacity to degrade EPX, removing 92.1% of EPX within 6 days. The temperature and pH were the two most important environmental factors affecting EPX degradation, followed by substrate concentration and inoculum dose. In addition, strain F1 has a high capacity to promote EPX degradation in soils, with a lower t_1/2 value (2.64 d) in F1-inoculated soil compared to the control (t_1/2 = 96.3 d) without strain F1. The strain could efficiently colonize rhizosphere soil and enhance degradation of EPX, leading to a significant decrease in the accumulation and translocation of EPX in vegetables, thereby alleviating the effects of EPX-induced stress on plants. Moreover, we observed that strain F1-gfp was able to colonize the roots, stems and leaves of Brassica rapa var. chinensis. Such colonization may play a role in the efficient degradation of EPX within plants. To our knowledge, this is the first study to demonstrate biodegradation of EPX in a soil-vegetable system using an EPX-degrading bacterium. This study indicates that strain F1 is a promising candidate for simultaneous bioremediation of soil contaminated with EPX and safe food production.

Soil bacterial community and metabolism showed a more sensitive response to PBAT biodegradable mulch residues than that of LDPE mulch residues

Biodegradable mulch film (BDM) is considered as an environmentally sustainable alternative to low density polyethylene (LDPE) mulch film. However, the low degradation rate of BDM resulted in residues in soil after service period which were similar to LDPE mulch film. Distinguishing the differential responses of crop growth, soil bacteria and metabolism to residues of BDM and LDPE mulch films is favourable for comparing the environmental toxicities of the two materials. The results indicated that emergence rate and yield of Chinese cabbage (Brassica campestris L. ssp. chinensis Makino) were significantly inhibited by two types mulch residues. BDM residues significantly decreased bacterial diversity by 1.2-2.3% through the enrichment of dominant phyla and inhibition of inferior phyla, while LDPE mulch residues not. The effects of BDM residues on soil metabolite spectrum were stronger than LDPE mulch residues with significant increase (3.9% 5.8%) in the abundance of total metabolites. Besides the pathways of metabolism, organismal systems, environmental information processing influenced by LDPE mulch resides, differential pathways including human diseases and cellular processes were also determined in soil with BDM residues. According to all the results of the present study, prior to the promotion of BDM, its influences on soil safety must be carefully investigated through critical and systematic research.

Succession of soil bacterial communities and network patterns in response to conventional and biodegradable microplastics: A microcosmic study in Mollisol

Significant soil contamination of microplastics (MPs) by the application of agricultural mulching films has aroused global concern, however, the effects of conventional and biodegradable MPs on the dynamics of soil microbial communities and network patterns have not been sufficiently reported. In this study, we conducted a soil microcosmic experiment by adding low-density polyethylene and biodegradable MPs (PE and BD) into a black soil at the dosages of 0 % (CK), 0.1 % (low-dose, w/w), 1 % (medium-dose, w/w) and 5 % (high-dose, w/w), and soils were sampled on the 15th, 30th, 60th and 90th day of soil incubation for high-throughput sequencing. The results showed that the incubation time was the most influential factor driving the variations in bacterial community structures, and significant effects of MP dosages and types were also detected. With the increase in MP dosage, bacterial diversity markedly increased and decreased at the beginning (D15) and end of sampling day (D90), respectively. Compared to CK, BD induced a larger community dissimilarity than PE and tended to enrich environmentally friendly taxa, while PE likely promoted the growth of hazardous taxa. Moreover, BD simplified interspecies interactions compared to the networks of PE and CK, and Nitrospira was identified as a keystone species in both PE and BD networks. These findings provide new insights into the influences of conventional and biodegradable MPs on the succession patterns of soil bacterial communities, and further studies are needed to explore the soil metabolic potentials affected by the presence of MPs.

Complete Genome Report of a Hydrocarbon-Degrading Sphingobium yanoikuyae S72

Sphingobium yanoikuyae S72 was isolated from the rhizosphere of sorghum plant in Mexico and we evaluated its survival and role in the degradation of some selected monoaromatic hydrocarbons and polycyclic aromatic hydrocarbons (PAHs) using minimal medium (Bushnell Hass medium (BH)) in which each of the hydrocarbons (naphthalene, phenanthrene, xylene, toluene, and biphenyl) served as sole carbon source. Gas column chromatography–mass spectrometry analysis was used to evaluate the effect of S72’s growth in the medium with the hydrocarbons. The genome of the S72 was sequenced to determine the genetic basis for the degradation of the selected hydrocarbon in S72. The genome was assembled de novo with Spades assembler and Velvet assembler and the obtained contigs were reduced to 1 manually using Consed software. Genome annotation was carried out Prokka version 1.12, and gene calling and further annotation was carried out with NCBI PGAAP. Pangenome analysis and COG annotation were done with bacteria pangenome analysis tool (BPGA) and with PATRIC online server, respectively. S72 grew effectively in the culture medium with the hydrocarbon with concentration ranging from 20–100 mg/mL for each hydrocarbon tested. S72 degraded biphenyl by 85%, phenanthrene by 93%, naphthalene by 81%, xylene by 19%, and toluene by 30%. The sequenced S72 genome was reduced to 1 contig and genome analysis revealed the presence of genes essential for the degradation of hydrocarbons in S72. A total of 126 unique genes in S72 are associated with the degradation of hydrocarbons and xenobiotics. S72 grew effectively in the tested hydrocarbon and shows good degradation efficiency. S72 will therefore be a good candidate for bioremediation of hydrocarbon contaminated soil.

A review of pristine and modified biochar immobilizing typical heavy metals in soil: Applications and challenges

In recent years, the application of biochar in the remediation of heavy metals (HMs) contaminated soil has received tremendous attention globally. We reviewed the latest research on the immobilization of soil HMs by biochar almost in the last 5 years (until 2021). The methods, effects and mechanisms of biochar and modified biochar on the immobilization of typical HMs in soil have been systematically summarized. In general, the HMs contaminating the soil can be categorized into two groups, the oxy-anionic HMs (As and Cr) and the cationic HMs (Pb, Cd, etc.). Reduction and precipitation of oxy-anionic HMs by biochar/modified biochar are the dominant mechanism for reducing HMs toxicity. Pristine biochar can effectively immobilize cationic HMs. The commonly applied modification method is to add substances that can precipitate HMs to the biochar. In addition, we assessed the risks of biochar applications. For instance, biochar may cause the leaching of certain HMs; biochar aging; co-transportation of biochar nanoparticles with HMs. Future work should focus on the artificial/intelligent design of biochar to make it suitable for remediation of multiple HMs contaminated soil.

Bacterial Biosorbents, an Efficient Heavy Metals Green Clean-Up Strategy: Prospects, Challenges, and Opportunities

Rapid industrialization has led to the pollution of soil and water by various types of contaminants. Heavy metals (HMs) are considered the most reactive toxic contaminants, even at low concentrations, which cause health problems through accumulation in the food chain and water. Remediation using conventional methods, including physical and chemical techniques, is a costly treatment process and generates toxic by-products, which may negatively affect the surrounding environment. Therefore, biosorption has attracted significant research interest in the recent decades. In contrast to existing methods, bacterial biomass offers a potential alternative for recovering toxic/persistent HMs from the environment through different mechanisms for metal ion uptake. This review provides an outlook of the advantages and disadvantages of the current bioremediation technologies and describes bacterial groups, especially extremophiles with biosorbent potential for heavy metal removal with relevant examples and perspectives.

Microbial Community and Function-Based Synthetic Bioinoculants: A Perspective for Sustainable Agriculture

Interactions among the plant microbiome and its host are dynamic, both spatially and temporally, leading to beneficial or pathogenic relationships in the rhizosphere, phyllosphere, and endosphere. These interactions range from cellular to molecular and genomic levels, exemplified by many complementing and coevolutionary relationships. The host plants acquire many metabolic and developmental traits such as alteration in their exudation pattern, acquisition of systemic tolerance, and coordination of signaling metabolites to interact with the microbial partners including bacteria, fungi, archaea, protists, and viruses. The microbiome responds by gaining or losing its traits to various molecular signals from the host plants and the environment. Such adaptive traits in the host and microbial partners make way for their coexistence, living together on, around, or inside the plants. The beneficial plant microbiome interactions have been exploited using traditional culturable approaches by isolating microbes with target functions, clearly contributing toward the host plants' growth, fitness, and stress resilience. The new knowledge gained on the unculturable members of the plant microbiome using metagenome research has clearly indicated the predominance of particular phyla/genera with presumptive functions. Practically, the culturable approach gives beneficial microbes in hand for direct use, whereas the unculturable approach gives the perfect theoretical information about the taxonomy and metabolic potential of well-colonized major microbial groups associated with the plants. To capitalize on such beneficial, endemic, and functionally diverse microbiome, the strategic approach of concomitant use of culture-dependent and culture-independent techniques would help in designing novel "biologicals" for various crops. The designed biologicals (or bioinoculants) should ensure the community's persistence due to their genomic and functional abilities. Here, we discuss the current paradigm on plant-microbiome-induced adaptive functions for the host and the strategies for synthesizing novel bioinoculants based on functions or phylum predominance of microbial communities using culturable and unculturable approaches. The effective crop-specific inclusive microbial community bioinoculants may lead to reduction in the cost of cultivation and improvement in soil and plant health for sustainable agriculture.

Root-associated (rhizosphere and endosphere) microbiomes of the Miscanthus sinensis and their response to the heavy metal contamination

The plant root-associated microbiomes, including both the rhizosphere and the root endosphere microbial community, are considered as a critical extension of the plant genome. Comparing to the well-studied rhizosphere microbiome, the understanding of the root endophytic microbiome is still in its infancy. Miscanthus sinensis is a pioneering plant that could thrive on metal contaminated lands and holds the potential for phytoremediation applications. Characterizing its root-associated microbiome, especially the root endophytic microbiome, could provide pivotal knowledge for phytoremediation of mine tailings. In the current study, M. sinensis residing in two Pb/Zn tailings and one uncontaminated site were collected. The results demonstrated that the metal contaminant fractions exposed strong impacts on the microbial community structures. Their influences on the microbial community, however, gradually decreases from the bulk soil through the rhizosphere soil and finally to the endosphere, which resulting in distinct root endophytic microbial community structures compared to both the bulk and rhizosphere soil. Diverse members affiliated with the order Rhizobiales was identified as the core microbiome residing in the root of M. sinensis. In addition, enrichment of plant-growth promoting functions within the root endosphere were predicted, suggesting the root endophytes may provide critical services to the host plant. The current study provides new insights into taxonomy and potential functions of the root-associated microbiomes of the pioneer plant, M. sinensis, which may facilitate future phytoremediation practices.

Combined Effects of Microplastics and Biochar on the Removal of Polycyclic Aromatic Hydrocarbons and Phthalate Esters and Its Potential Microbial Ecological Mechanism

Microplastics (MPs) have been attracting wide attention. Biochar (BC) application could improve the soil quality in the contaminated soil. Currently, most studies focused on the effect of MPs or BC on the soil properties and microbial community, while they neglected the combined effects. This study investigated the combined effects of BC or ball-milled BC (BM) and polyethylene plastic fragments (PEPFs) and degradable plastic fragments (DPFs) on the removal of polycyclic aromatic hydrocarbons (PAHs) and phthalate esters (PAEs) from the PAH-contaminated soil and the potential microbial ecological mechanisms. The results showed that BC or BM combined with PEPF could accelerate the removal of PAHs and PAEs. PEPF combined with BM had the most significant effect on the removal of PAHs. Our results indicating two potential possible reasons contribute to increasing the removal of organic pollutants: (1) the high sorption rate on the PEPF and BC and (2) the increased PAH-degrader or PAE-degrader abundance for the removal of organic pollutants.

Priming Effects of Cover Cropping on Bacterial Community in a Tea Plantation

The acidic nature of red soil commonly found in tea plantations provides unique niches for bacterial growth. These bacteria as well as soil properties are dynamic and vary with agricultural management practices. However, less is known about the influence of manipulation such as cover cropping on bacterial communities in tea plantations. In this study a field trial was conducted to address the short-term effects of soybean intercropping on a bacterial community. Diversity, metabolic potential and structure of the bacterial community were determined through community level physiological profiling and amplicon sequencing approaches. Cover cropping was observed to increase soil EC, available P, K, and microelements Fe, Mn, Cu, and Zn after three months of cultivation. Bacterial functional diversity and metabolic potential toward six carbon source categories also increased in response to cover cropping. Distinct bacterial communities among treatments were revealed, and the most effective biomarkers, such as Acidobacteriaceae, Burkholderiaceae, Rhodanobacteraceae, and Sphingomonadaceae, were identified in cover cropping. Members belonging to these families are considered as organic matter decomposers and/or plant growth promoting bacteria. We provided the first evidence that cover cropping boosted both copiotrophs (Proteobacteria) and oligotrophs (Acidobacteria), with potentially increased functional stability, facilitated nutrient cycling, and prospective benefits to plants in the tea plantation.

Microplastic pollution and its relationship with the bacterial community in coastal sediments near Guangdong Province, South China

The ecological stress caused by microplastic (MP) pollution in marine environments has attracted global attention. However, few studies have investigated the relationship between MP pollution and the microbial community in natural sediments. This study was the first to systematically characterize MP pollution (i.e., its abundance, shape, size and color) and investigate its relationship with the bacterial community in coastal sediments from Guangdong, South China, by microscopic observation and Illumina sequencing. The results of this study indicated that the abundance of microplastics (MPs), which was 344 ± 24 items/kg in 33 coastal sediments from 11 sites from South China, represented a relatively high level of MP pollution. MPs with sizes of <0.5 m, 0.5-1.0 mm and 1-2 mm accounted for the highest proportion (75%) in the sediments. Fiber/film (82%) and white/blue (91%) were the dominant shapes and colors, respectively, in all MP samples. Furthermore, the abundances, three shapes (fiber, film and fragment), three sizes (<0.5 mm, 0.5-1.0 mm and 1-2 mm), and two colors (blue and white) of MPs displayed positive correlations with some potential pathogens, including Vibrio, Pseudomonas, Bacillus and Streptococcus, but exhibited negative correlations with an environmentally friendly bacterial genus, Sphingomonas (which degrades various hazardous organic compounds), indicating that MPs might increase the potential ecological risks of coastal sediments. Our results may help to elucidate the relationship between MP pollution and the microbial community in coastal sediments.

Biochar-bacteria-plant partnerships: Eco-solutions for tackling heavy metal pollution

Over the past 30 years, the ever-rising demands of the modern and growing population have led to the rapid development of agricultural and industrial sectors worldwide. However, this expansion has exposed the environment to various pollutants including heavy metal (HM)s. Almost all HMs are serious toxicants and can pose serious health risks to living organisms in addition to their bioaccumulative and non-biodegradable nature. Different techniques have been developed to restore the ecological functions of the HM-contaminated soil (HMCS). However, the major downfalls of the commonly used remediation technologies are the generation of secondary wastes, high operating costs, and high energy consumption. Phytoremediation is a prominent approach that is more innocuous than the existing remediation approaches. Some microbes-plant interactions enhance the bioremediation process, with heavy metal resistant-plant growth promoting bacteria (HMRPGPB) being widely used to assist phytoremediation of HMs. However, the most common of all major microbial assisted-phytoremediation disturbances is that the HM-contaminated soil is generally deficient in nutrients and cannot sustain the rapid growth of the applied HMRPGPB. In this case, biochar has recently been approved as a potential carrier of microbial agents. The biochar-HMRPGPB-plant association could provide a promising green approach to remediate HM-polluted sites. Therefore, this review addresses the mechanisms through which biochar and HMRPGPB can enhance phytoremediation. This knowledge of biochar-HMRPGPB-plant interactions is significant with respect to sustainable management of the HM-polluted environment in terms of both ecology and economy, and it offers the possibility of further development of new green technologies.

Extremophilic Microorganisms for the Treatment of Toxic Pollutants in the Environment

As concerns about the substantial effect of various hazardous toxic pollutants on the environment and public health are increasing, the development of effective and sustainable treatment methods is urgently needed. In particular, the remediation of toxic components such as radioactive waste, toxic heavy metals, and other harmful substances under extreme conditions is quite difficult due to their restricted accessibility. Thus, novel treatment methods for the removal of toxic pollutants using extremophilic microorganisms that can thrive under extreme conditions have been investigated during the past several decades. In this review, recent trends in bioremediation using extremophilic microorganisms and related approaches to develop them are reviewed, with relevant examples and perspectives.

Isolation and characterization of a novel Sphingobium yanoikuyae strain variant that uses biohazardous saturated hydrocarbons and aromatic compounds as sole carbon sources

Background: Green micro-alga, Chlamydomonas reinhardtii (a Chlorophyte), can be cultured in the laboratory heterotrophically or photo-heterotrophically in Tris- Phosphate- Acetate (TAP) medium, which contains acetate as the carbon source. Chlamydomonas can convert acetate in the TAP medium to glucose via the glyoxylate cycle, a pathway present in many microbes and higher plants. A novel bacterial strain, CC4533, was isolated from a contaminated TAP agar medium culture plate of a Chlamydomonas wild type strain. In this article, we present our research on the isolation, and biochemical and molecular characterizations of CC4533.

Methods: We conducted several microbiological tests and spectrophotometric analyses to biochemically characterize CC4533. The 16S rRNA gene of CC4533 was partially sequenced for taxonomic identification. We monitored the growth of CC4533 on Tris-Phosphate (TP) agar medium (lacks a carbon source) containing different sugars, aromatic compounds and saturated hydrocarbons, to see if CC4533 can use these chemicals as the sole source of carbon.

Results: CC4533 is a Gram-negative, non-enteric yellow pigmented, aerobic, mesophilic bacillus. It is alpha-hemolytic and oxidase-positive. CC4533 can ferment glucose, sucrose and lactose, is starch hydrolysis-negative, resistant to penicillin, polymyxin B and chloramphenicol. CC4533 is sensitive to neomycin. Preliminary spectrophotometric analyses indicate that CC4533 produces b-carotenes. NCBI-BLAST analyses of the partial 16S rRNA gene sequence of CC4533 show 99.55% DNA sequence identity to that of Sphingobium yanoikuyae strain PR86 and S. yanoikuyae strain NRB095. CC4533 can use cyclo-chloroalkanes, saturated hydrocarbons present in car motor oil, polyhydroxyalkanoate, and mono- and poly-cyclic aromatic compounds, as sole carbon sources for growth.

Conclusions: Taxonomically, CC4533 is very closely related to the alpha-proteobacterium S. yanoikuyae, whose genome has been sequenced. Future research is needed to probe the potential of CC4533 for environmental bioremediation. Whole genome sequencing of CC4533 will confirm if it is a novel strain of S. yanoikuyae or a new Sphingobium species.

Modeling and Cr(VI) ion uptake kinetics of Sorghum bicolor plant assisted by plant growth-promoting Pannonibacter phragmetitus: an ecofriendly approach

The research work focuses on the application of Cr(VI)-resistant plant growth-promoting bacteria Pannonibacter phragmetitus for enhancing Cr(VI) uptake by Sorghum bicolor. Significant increase in plant shoot and root characters was found when assisted by P. phragmetitus. The obtained strain showed 700 mg/L of chromium reduction at 24-h incubation. Indole-3 acetic acid (IAA) production by the bacterial strain was found to be 86.45 μg/mL. Pannonibacter phragmetitus solubilized tricalcium phosphate showing maximum solubilizing activity of PSI = 3.31. The q_max of P. phragmetitus was high in the wavelength of 600 nm. Langmuir isotherm best described the Cr(VI) ion uptake by the plant. The R_L values reliably reduced with expanding Cr(VI) ion concentration from 25 to 150 mg/L. The outcomes of kinetic studies showed that compared with pseudo first-order, pseudo second-order kinetics better describes the plant Cr(VI) uptake rate. Elovich model describes the increased rates for attaining equilibrium. The equilibrium parameter values for different Cr(VI) ion concentrations range between 0 and 1 which describes the favorable condition for plant metal uptake at different concentrations. Graphical abstract.

Bacteria Sphingobium yanoikuyae Sy310 enhances accumulation capacity and tolerance of cadmium in Salix matsudana Koidz roots

Phytoremediation assisted by plant growth-promoting bacteria (PGPB) is considered an effective strategy for cadmium (Cd) removal in contaminated sites. This study uses a hydroponic experiment to investigate how Sphingobium yanoikuyae Sy310 affects Cd accumulation capacity and tolerance of Salix matsudana Koidz (S. matsudana) roots. The results showed that Cd induced growth change and physiological response on S. matsudana roots, displaying with reduced root length, increased antioxidant enzyme activities, and most importantly, enhanced cell wall polysaccharide contents. The Sy310 inoculation enhanced Cd accumulation in roots and alleviated the Cd toxic effects by regulating root growth, antioxidant enzyme system, and cell wall polysaccharide remodeling. Under Cd stress, Sy310 significantly induced increased root length and biomass, as well as higher root IAA level and Cd retention in cell walls. The Sy310 inoculation enhanced root pectin and hemicellulose 1 content, and pectin methylesterase activity, indicating that more amount of -COOH and -OH in cell walls for binding Cd. With Sy310-regulated extensive Cd regional sequestration in root cell walls and enhanced catalase activity, the root H₂O₂ and malondialdehyde content decreased, which contributes to improve Cd tolerance of S. matsudana roots. Furthermore, the Sy310 inoculation did not affect root cell wall structure and oxidative stress in the absence of Cd, representing a well-symbiotic relationship between Sy310 and S. matsudana. Therefore, Sy310 plays an important role in expediting the phytoremediation process of Cd with S. matsudana and has practical application potential.

Transfer of Sphingorhabdus marina, Sphingorhabdus litoris, Sphingorhabdus flavimaris and Sphingorhabdus pacifica corrig. into the novel genus Parasphingorhabdus gen. nov. and Sphingopyxis baekryungensis into the novel genus Novosphingopyxis gen. nov. within the family Sphingomonadaceae

During a phylogenetic analysis of Sphingorhabdus and its closely related genera in the family Sphingomonadaceae, we found that the genus Sphingorhabdus and the species Sphingopyxis baekryungensis might not be properly assigned in the taxonomy. Phylogenetic, phenotypic and chemotaxonomic characterizations clearly showed that the genus Sphingorhabdus should be reclassified into two genera (Clade I and Clade II), for which the original genus name, Sphingorhabdus, is proposed to be retained only for Clade I, and a new genus named as Parasphingorhabdus gen. nov. is proposed for Clade II with four new combinations: Parasphingorhabdus marina comb. nov., Parasphingorhabdus litoris comb. nov., Parasphingorhabdus flavimaris comb. nov. and Parasphingorhabdus pacifica comb. nov. Moreover, Sphingopyxis baekryungensis should represent a novel genus in the family Sphingomonadaceae, for which the name Novosphingopyxis gen. nov. is proposed, with a combination of Novosphingopyxis baekryungensis comb. nov. The study provides a new insight into the taxonomy of closely related genera in the family Sphingomonadaceae.

Biodiversity and ecology of microorganisms in high pressure membrane filtration systems

High-pressure membrane filtration (reverse osmosis and nanofiltration) is used to purify different water sources, including wastewater, surface water, groundwater and seawater. A major concern in membrane filtration is the accumulation and growth of micro-organisms and their secreted polymeric substances, leading to reduced membrane performance and membrane biofouling. The fundamental understanding of membrane biofouling is limited despite years of research, as the means of microbial interactions and response to the conditions on the membrane surface are complicated. Here, we discuss studies that investigated the microbial diversity of fouled high-pressure membranes. High-throughput amplicon sequencing of the 16S rRNA gene have shown that Burkholderiales, Pseudomonadales, Rhizobiales, Sphingomonadales and Xanthomonadales frequently obtain a high relative abundance on fouled membranes. The bacterial communities present in the diverse feed water types and in pre-treatment compartments are different from the communities on the membrane, because high-pressure membrane filtration provides a selective environment for certain bacterial groups. The biofilms that form within the pre-treatment compartments do not commonly serve as an inoculum for the subsequent high-pressure membranes. Besides bacteria also fungi are detected in the water treatment compartments. In contrast to bacteria, the fungal community does not change much throughout membrane cleaning. The stable fungal diversity indicates that they are more significant in membrane biofouling than previously thought. By reviewing the biodiversity and ecology of microbes in the whole high pressure membrane filtration water chain, we have been able to identify potentials to improve biofouling control. These include modulation of hydrodynamic conditions, nutrient limitation and the combination of cleaning agents to target the entire membrane microbiome.

Response of soil enzyme activities and bacterial communities to the accumulation of microplastics in an acid cropped soil

The ecological stress of microplastics (MPs) contamination in agroecosystems raise worldwide concerns. However very few studies concentrated on the effects of MPs exposure on soil microbial community. The alterations of enzymatic activities and bacterial communities were assayed by spiking 1% and 5% (w/w) of polyethylene (PE) and polyvinyl chloride (PVC) MPs in an acid soil. The results showed that both PE and PVC addition inhibited fluorescein diacetate hydrolase activity and stimulated urease and acid phosphatase activities, and declined the richness and diversity of the bacterial communities. More severe effects were observed in the PE treated soils compared to the PVC treated soils generally. The relative abundances of families Burkholderiaceae increased significantly (p < .05) after MPs addition, suggesting the bacteria associated with nitrogen fixation stimulated by the MPs input. Meanwhile, significant (p < .05) decline of Sphingomonadaceae and Xanthobacteraceae after addition of 5% PVC and 1% PE MPs, respectively implied that MPs might inhibit the biodegradation of xenobiotics in the soil. Mover, the PICRUSt analysis demonstrated that membrane transporter was a sensitive prediction functional gene of microplastics exposure in the soil. Future studies could be focused on the role of MPs on the regulation of nitrogen cycling and organic compounds degradation in soils.

Sphingomonas solaris sp. nov., isolated from a solar panel in Boston, Massachusetts

Solar panel surfaces, although subjected to a range of extreme environmental conditions, are inhabited by a diverse microbial community adapted to solar radiation, desiccation and temperature fluctuations. This is the first time a new bacterial species has been isolated from this environment. Strain R4DWN^T belongs to the genus Sphingomonas and was isolated from a solar panel surface in Boston, MA, USA. Strain R4DWN^T is a Gram-negative, non-motile and rod-shaped bacteria that tested positive for oxidase and catalase and forms round-shaped, shiny and orange-coloured colonies. It is mesophilic, neutrophilic and non-halophilic, and presents a more stenotrophic metabolism than its closest neighbours. The major fatty acids in this strain are C_18:1ω7c/C_18:1ω6c, C_16:1ω7c/C_16:1ω6c, C_14:0 2OH and C_16:0. Comparison of 16S rRNA gene sequences revealed that the closest type strains to R4DWN^T are Sphingomonas fennica, Sphingomonas formosensis, Sphingomonas prati, Sphingomonas montana and Sphingomonas oleivorans with 96.3, 96.1, 96.0, 95.9 and 95.7 % pairwise similarity, respectively. The genomic G+C content of R4DWN^T is 67.9 mol%. Based on these characteristics, strain R4DWN^T represents a novel species of the genus Sphingomonas for which the name Sphingomonas solaris sp. nov. is proposed with the type strain R4DWN^T (=CECT 9811^T=LMG 31344^T).

Long-term phytomanagement with compost and a sunflower - Tobacco rotation influences the structural microbial diversity of a Cu-contaminated soil

At a former wood preservation site contaminated with Cu, various phytomanagement options have been assessed in the last decade through physicochemical, ecotoxicological and biological assays. In a field trial at this site, phytomanagement with a crop rotation based on tobacco and sunflower, combined with the incorporation of compost and dolomitic limestone, has proved to be efficient in Cu-associated risk mitigation, ecological soil functions recovery and net gain of economic and social benefits. To demonstrate the long-term effectiveness and sustainability of phytomanagement, we assessed here the influence of this remediation option on the diversity, composition and structure of microbial communities over time, through a metabarcoding approach. After 9 years of phytomanagement, no overall effect was identified on microbial diversity; the soil amendments, notably the repeated compost application, led to shifts in soil microbial populations. This phytomanagement option induced changes in the composition of soil microbial communities, promoting the growth of microbial groups belonging to Alphaproteobacteria, many being involved in N cycling. Populations of Nitrososphaeria, which are crucial in nitrification, as well as taxa from phyla Planctomycetacia, Chloroflexi and Gemmatimonadetes, which are tolerant to metal contamination and adapted to oligotrophic soil conditions, decreased in amended phytomanaged plots. Our study provides an insight into population dynamics within soil microbial communities under long-term phytomanagement, in line with the assessment of soil ecological functions and their recovery.

Endophytic Bacteria in in planta Organopollutant Detoxification in Crops

Microbe-assisted organopollutant removal, or in planta crop decontamination, is based on an interactive system between organopollutant-degrading endophytic bacteria (DEB_OP) and crops in alleviating organic toxins in plants. This script focuses on the fast-growing body of literature that has recently bloomed in organopollutant control in agricultural plants. The various facets of DEB_OP under study include their colonization, distribution, plant growth-promoting mechanisms, and modes of action in the detoxification process in plants. Also, an assessment of the biotechnological advances, advantages, and bottlenecks in accelerating the implementation of this decontamination strategy will be undertaken. The highlighted key research directions from this review will shape the future of agro-environmental sustainability and preservation of human health.