Secondary metabolites released by the rhizosphere bacteria Arthrobacter oxydans and Kocuria rosea enhance plant availability and soil-plant transfer of germanium (Ge) and rare earth elements (REEs)

Rare earth elements redistribution in mine tailings soil: A comparative study of sunlit and shady slopes after in-situ leaching

The in-situ leaching of rare earth minerals results in ecological differences between sunlit and shady slopes, which may be related to differences in the distribution REEs in the associated soil matrices. Studies of REEs mine tailings in Southern China indicated higher total concentrations of REEs on sunlit slopes compared to shady ones. Specifically, the exchangeable REEs fraction (F1-REEs) was higher on the shady slopes, whereas the Fe/Mn oxides bound REEs fraction (F3-REEs) was higher on the sunlit slopes. In addition, light REE (LREE) concentrations were lower at lower elevations. With the exception of the Ce fraction which remained stable, this indicated a change in all REEs distributions, moving from F1-REEs towards the residual fraction. Hierarchical cluster and principal component analysis revealed a strong correlation between F3-REEs, organic matter bound REEs (F4-REEs), and LREEs, and a positive association of F3-REEs with sunlight exposure. Partial Least Squares Path Modeling analysis suggested that OM promoted the conversion of LREEs to F3 and F4-REEs in soil driven by sunlight exposure. Additionally, as the Feo/Fed ratio decreased, more LREEs were converted to F3. This study suggests that sunlight and elevation both play a critical role in the geochemical dynamics of REEs in in-situ tailings, advocating for environmental evaluations to be undertaken in order to accurately understand the ecological impacts of rare earth mining.

A systematic review and meta-analysis on the root effects and toxic mechanisms of rare earth elements

Rare earth elements (REEs) have attracted much attention because of their unique physical and chemical properties. The root system is the plant organ most directly in contact with REEs, and it is critical to understand the mechanisms of interaction between the two. This paper investigates the effects of REEs on plant enrichment and fractionation, as well as on various developmental and toxicity indices of the root system. REEs are more likely to be deposited on the root surface under the influence of root secretion. The complexation between the two affects the uptake and fractionation of REEs and the altered pattern of root secretion. The toxicity mechanisms of REEs on plant root cells were lied in: (1) REEs generate reactive oxygen species after entering the plant, leading to oxidative stress and damage to plant cells; (2) REEs with higher charge-to-volume ratios compete for organic ligands with or displace Ca2+, further disrupting the normal function of plant root cells. It was shown that the sensitivity of inter-root microorganisms to REEs varied depending on the content and physicochemical properties of REEs. The paper also concluded with a meta-analysis of phytotoxicity induced by REEs, which showed that REEs affect plant physiological parameters. REEs, as a source of oxidative stress, triggered lipid peroxidation damage in plants and enhanced the activity of antioxidant enzymes, thus revealing the significant toxicity of REEs to plants. The phytotoxic effects of REEs increased with time and concentration. These results help to elucidate the ecotoxicology of rare earth-induced phytotoxicity.

Performance and mechanistic study of biochar and magnesium-enhanced phytoremediation in cadmium-contaminated soil by alfalfa

Recently, phytoremediation has been regarded as a green and environment friendly technique to treat metals contaminated soils. Thus, in this study, pot experiments were designed to investigate the combine effects of biochar and magnesium (MPs) to purify cadmium (Cd)-contaminated soils by Medicago sativa L. (alfalfa). The results showed that the combined use of biochar and Mg significantly increased the accumulation of Cd and promoted the transport of Cd from root to shoot in alfalfa, simultaneously. Importantly, the combined use of biochar and Mg could increase the accumulation of Cd in shoot and whole plant (shoot + root) of alfalfa up-to 59.1% and 23.1%, respectively. Moreover, the enhancement mechanism can be analyzed from several aspects. Firstly, the photosynthesis was enhanced, which was beneficial to plant growth. The product of photosynthesis provided energy for uptake and transport of Cd. Meanwhile, its transport in phloem could promote the transport of Cd. Secondly, the enhancement of antioxidant capacity of alfalfa effectively protected the membrane structure of alfalfa, which indicated that Cd could enter alfalfa from the channel on the cell membrane. Lastly, the chemical form of Cd and microbial community structure in soil were changed. Overall, these changes reduced the Cd toxicity in soil, enhanced the resistance capability of alfalfa, increased the Cd uptake by alfalfa and promoted the growth of alfalfa. Thus, the obtained results suggested that the combined use of biochar and Mg is an effective approach to enhance phytoremediation performance for purifying Cd-contaminated soils.

Isolation, Selection, and Identification of Keratinolytic Bacteria for Green Management of Keratin Waste

The volume of difficult-to-process keratin waste is increasing as a result of rising global meat production. If not properly managed, this waste can contribute to environmental pollution and pose a threat to human and animal welfare. An interesting and more sustainable alternative is therefore the bioconversion of keratin using microorganisms and their enzymes. This work aimed to isolate bacteria from soil samples and zoonotic keratins and to evaluate their enzymatic capacity to degrade α- and β-keratin wastes. A total of 113 bacterial strains were isolated from environmental samples and subjected to taxonomic identification using the MALDI-TOF MS technique and to a two-step screening for proteolytic and keratinolytic activity. The ability to degrade a β-rich keratin substrate was observed in almost all of the strains isolated from soil and horsehairs. In contrast, when an α-rich keratin substrate was used, the highest levels of hydrolysis were observed only for Ker39, Ker66, Ker85, Ker100, and Ker101. Strains with the highest biodegradation potential were identified using molecular biology methods. Phylogenetic analysis of 16S rDNA gene sequences allowed the assignment of selected keratinolytic microorganisms to the genera Exiguobacterium, Priestia, Curtobacterium, Stenotrophomonas, Bacillus, Kocuria, or Pseudomonas. The results of this study are a promising precursor for the development of new, more sustainable methods of managing keratin waste to produce high-value hydrolysates.

Siderophores and metallophores: Metal complexation weapons to fight environmental pollution

Siderophores are small molecules of organic nature, released by bacteria to chelate iron from the surrounding environment and subsequently incorporate it into the cytoplasm. In addition to iron, these secondary metabolites can complex with a wide variety of metals, which is why they are commonly studied in the environment. Heavy metals can be very toxic when present in large amounts on the planet, affecting public health and all living organisms. The pollution caused by these toxic metals is increasing, and therefore it is urgent to find practical, sustainable, and economical solutions for remediation. One of the strategies is siderophore-assisted bioremediation, an innovative and advantageous alternative for various environmental applications. This research highlights the various uses of siderophores and metallophores in the environment, underscoring their significance to ecosystems. The study delves into the utilization of siderophores and metallophores in both marine and terrestrial settings (e.g. bioremediation, biocontrol of pathogens, and plant growth promotion), such as bioremediation, biocontrol of pathogens, and plant growth promotion, providing context for the different instances outlined in the existing literature and highlighting their relevance in each field. The study delves into the structures and types of siderophores focusing on their singular characteristics for each application and methodologies used. Focusing on recent developments over the last two decades, the opportunities and challenges associated with siderophores and metallophores applications in the environment were mapped to arm researchers in the fight against environmental pollution.

A Practical Toolkit for the Detection, Isolation, Quantification, and Characterization of Siderophores and Metallophores in Microorganisms

Siderophores are well-recognized low-molecular-weight compounds produced by numerous microorganisms to acquire iron from the surrounding environments. These secondary metabolites can form complexes with other metals besides iron, forming soluble metallophores; because of that, they are widely investigated in either the medicinal or environmental field. One of the bottlenecks of siderophore research is related to the identification of new siderophores from microbial sources. Herein we have compiled a comprehensive range of standard and updated methodologies that have been developed over the past few years to provide a comprehensive toolbox in this area to current researchers.

Draft genome sequence of Arthrobacter sp. strain B10-11 isolated from the tomato rhizosphere

In the present work, we present the draft genome sequence of a new putative Arthrobacter species associated with the tomato rhizosphere.

Uptake and transport mechanisms of rare earth hyperaccumulators: A review

Due to their use in a number of advanced electronic technologies, Rare earth elements (REEs) have recently emerged as a key strategic resource for many nations worldwide. The significant increase in demand for REEs has thus greatly increased the mining of these substances, but this industrial-scale expansion of mining activities also poses potential risks to the surrounding environment, flora, fauna, and humans. Hence efficient REE remediation is one potential remediation process involving in situ clean-up of contaminated soil which has gained much attention in recent years, due to its low cost and lack of secondary pollution. However, some crucial aspects of phytoremediation, such as the precise-mechanisms of absorption, transport, and tolerance of REEs by hyperaccumulators -are poorly understood. This review briefly discusses the environmental risks associated with excess REEs, the efficacy of phytoremediation technologies coupled with, appropriate hyperaccumulator species to migrate REEs exposure. While REEs hyperaccumulator species should ideally be large-biomass trees and shrubs suitable for cropping in subtropical regions areas, such species have not yet been found. Specifically, this review focuses on the factors affecting the bioavailability of REEs in plants, where organic acids are critical ligands promoting efficient transport and uptake. Thus the uptake, transport, and binding forms of REEs in the above-ground parts of hyperaccumulators, especially the transporters isolated from the heavy metal transporter families, are discussed in detail. Finally, having summarized the current state of research in this area, this review proceeds to discuss current knowledge gaps and research directions. With a focus on hyperaccumulators, this review serves as a basis for future phytoremediation strategies of rare earth mining-impacted environments and addresses ecosystem/environmental degradation issues resulting from such mining activity.

Mercapto-based palygorskite modified soil micro-biology and reduced the uptake of heavy metals by Salvia miltiorrhiza in cadmium and lead co-contaminated soil

Salvia miltiorrhiza is an important traditional Chinese medicinal and edible plant that can easily accumulate excessive cadmium (Cd) and lead (Pb) from contaminated soils. The soil contaminated with heavy metals severely threatened the quality of S. miltiorrhiza products. In this study, we investigated the effects of mercapto-based palygorskite (MPAL), a new passivation amendment, on restraining the uptake of Cd and Pb by S. miltiorrhiza, and the impact on soil micro-ecology. Results showed that the application of MPAL prominently enhanced the biomass and antioxidant enzyme activities of S. miltiorrhiza. With the treatment of 4% MPAL, the Cd and Pb contents in the roots were significantly decreased by 81.42% and 69.09%, respectively. The active ingredients of S. miltiorrhiza, including Danshensu, Cryptotanshinone, Tanshinone I and Tanshinone II were remarkedly increased by 1899.46%, 5838.64%, 54.23% and 200.78%, respectively. In addition, MPAL decreased the bio-availability of Cd and Pb by speciation transformation, which simultaneously boosted the activities of cellulase and sucrase. The application of MPAL also improved the bacterial community composition. These findings revealed that the application of MPAL regulated the soil micro-ecology, positively modified the growth and obstructed the Cd and Pb accumulation in S. miltiorrhiza.

A virus induces alterations in root morphology while exerting minimal effects on the rhizosphere and endosphere microorganisms in rice

The highly destructive southern rice black-streaked dwarf virus (SRBSDV) causes significant losses in rice production. To understand its impact on rice root, we studied fibrous root development and root microbiota variation (rhizosphere and endosphere) after SRBSDV infection. SRBSDV infection reduced the number and length of fibrous roots in rice. Interestingly, the rhizosphere had higher bacterial diversity and abundance at the initial (0 days) and 30-day postinfection stages, while 30-day-old roots showed increased diversity and abundance. However, there were no significant differences in microbiota diversity between infected and noninfected rice plants. The major rhizosphere microbiota included Proteobacteria, Bacteroidota, Acidobacteriota, and Planctomycetota, comprising about 80% of the community. The endosphere was dominated by Proteobacteria and Cyanobacteria, constituting over 90%, with Bacteroidota as the next most prominent group. Further, we identified differentially expressed genes related to plant-pathogen interactions, plant hormone signal, and ABC transporters, potentially affecting root morphology. Notably, specific bacteria (e.g. Inquilinus and Actinoplanes) showed correlations with these pathways. In conclusion, SRBSDV primarily influences root growth through host metabolism, rather than exerting direct effects on the root microbiota. These insights into the interactions among the pathogen, rice plant, and associated microbiota could have implications for managing SRBSDV's detrimental effects on rice production.

Biochar immobilized plant growth-promoting rhizobacteria enhanced the physicochemical properties, agronomic characters and microbial communities during lettuce seedling

Spent mushroom substrate (SMS) is the by-products of mushroom production, which is mainly composed of disintegrated lignocellulosic biomass, mushroom mycelia and some minerals. The huge output and the lack of effective utilization methods make SMS becoming a serious environmental problem. In order to improve the application of SMS and SMS derived biochar (SBC), composted SMS (CSMS), SBC, combined plant growth-promoting rhizobacteria (PGPR, Bacillus subtilis BUABN-01 and Arthrobacter pascens BUAYN-122) and SBC immobilized PGPR (BCP) were applied in the lettuce seedling. Seven substrate treatments were used, including (1) CK, commercial control; (2) T1, CSMS based blank control; (3) T2, T1 with combined PGPR (9:1, v/v); (4) T3, T1 with SBC (19:1, v/v); (5) T4, T1 with SBC (9:1, v/v); (6) T5, T1 with BCP (19:1, v/v); (7) T6, T1 with BCP (9:1, v/v). The physicochemical properties of substrate, agronomic and physicochemical properties of lettuce and rhizospheric bacterial and fungal communities were investigated. The addition of SBC and BCP significantly (p < 0.05) improved the total nitrogen and available potassium content. The 5% (v/v) BCP addiction treatment (T5) represented the highest fresh weight of aboveground and underground, leave number, chlorophyll content and leaf anthocyanin content, and the lowest root malondialdehyde content. Moreover, high throughput sequencing revealed that the biochar immobilization enhanced the adaptability of PGPR. The addition of PGPR, SBC and BCP significantly enriched the unique bacterial biomarkers. The co-occurrence network analysis revealed that 5% BCP greatly increased the network complexity of rhizospheric microorganisms and improved the correlations of the two PGPR with other microorganisms. Furthermore, microbial functional prediction indicated that BCP enhanced the nutrient transport of rhizospheric microorganisms. This study showed the BCP can increase the agronomic properties of lettuce and improve the rhizospheric microbial community.

Biochar-immobilized Bacillus megaterium enhances Cd immobilization in soil and promotes Brassica chinensis growth

Phosphate solubilizing bacteria (PSB) has been considered an environmental-friendly phosphate fertilizer without cadmium (Cd) input into soils, but its possibility of Cd fixation in soil needs to be explored. Since direct inoculation results in a rapid decline of the population and activity, we immobilized Bacillus megaterium with maize straw biochar (B-PSB) and investigated its feasibility in remediating Cd-contaminated soil. Pot experiments showed that the application of B-PSB significantly ameliorated the growth of Brassica chinensis under Cd stress, with a fresh weight increased by 59.08% compared to the Cd-control. B-PSB reduced Cd accumulation in Brassica chinensis by 61.69%, and promoted the uptake of P and N by 134.97% and 98.71% respectively. Microbial community analysis showed B-PSB recruited more plant growth-promoting bacteria in near-rhizosphere soil, which provides a favorable microenvironment for both PSB and crops. Column leaching experiments verified that B-PSB achieved the dissolution of stable P while fixing Cd. Batch tests further revealed that biochar served as a successful carrier facilitating the growth of B. megaterium and Cd immobilization. Given the widespread Cd contamination in agricultural soils, our results indicate that B-PSB is a promising soil amendment to secure food safety.

Genomic, Molecular, and Phenotypic Characterization of Arthrobacter sp. OVS8, an Endophytic Bacterium Isolated from and Contributing to the Bioactive Compound Content of the Essential Oil of the Medicinal Plant Origanum vulgare L

Medicinal plants play an important role in the discovery of new bioactive compounds with antimicrobial activity, thanks to their pharmacological properties. However, members of their microbiota can also synthesize bioactive molecules. Among these, strains belonging to the genera Arthrobacter are commonly found associated with the plant's microenvironments, showing plant growth-promoting (PGP) activity and bioremediation properties. However, their role as antimicrobial secondary metabolite producers has not been fully explored. The aim of this work was to characterize the Arthrobacter sp. OVS8 endophytic strain, isolated from the medicinal plant Origanum vulgare L., from molecular and phenotypic viewpoints to evaluate its adaptation and influence on the plant internal microenvironments and its potential as a producer of antibacterial volatile molecules (VOCs). Results obtained from the phenotypic and genomic characterization highlight its ability to produce volatile antimicrobials effective against multidrug-resistant (MDR) human pathogens and its putative PGP role as a producer of siderophores and degrader of organic and inorganic pollutants. The outcomes presented in this work identify Arthrobacter sp. OVS8 as an excellent starting point toward the exploitation of bacterial endophytes as antibiotics sources.

Distribution of rare earth elements (REEs) and their roles in plant growth: A review

The increasing use of rare earth elements (REEs) in various industries has led to a rise in discharge points, thus increasing discharge rates, circulation, and human exposure. Therefore, REEs have received widespread attention as important emerging pollutants. This article thus summarizes and discusses the distribution and occurrence of REEs in the world's soil and water, and briefly introduces current REEs content analysis technology for the examination of different types of samples. Specifically, this review focuses on the impact of REEs on plants, including the distribution and fractionation of REEs in plants and their bioavailability, the effect of REEs on seed germination and growth, the role of REEs in plant resistance, the physiological and biochemical responses of plants in the presence of REEs, including mineral absorption and photosynthesis, as well as a description of the substitution mechanism of REEs competing for Ca in plant cells. Additionally, this article summarizes the potential mechanisms of REEs to activate endocytosis in plants and provides some insights into the mechanisms by which REEs affect endocytosis from a cell and molecular biology perspective. Finally, this article discusses future research prospects and summarizes current scientific findings that could serve as a basis for the development of more sustainable rare earth resource utilization strategies and the assessment of REEs in the environment.

Field Studies on the Effect of Bioaugmentation with Bacillus amyloliquefaciens FZB42 on Plant Accumulation of Rare Earth Elements and Selected Trace Elements

This study is an investigation of the effect of soil bioaugmentation (inoculation) on a field scale with the commercially available product RhizoVital®42, containing Bacillus amyloliquefaciens FZB4, on element bioavailability, plant biomass production, as well as accumulation of rare earth elements (REEs), germanium, and selected trace elements. Zea mays and Helianthus annuus were selected as test plants. Post-harvest, results showed inoculation increased biomass production of Z. mays and H. annuus by 24% and 26%, albeit insignificant at p ≤ 0.05. Bioaugmentation enhanced Z. mays shoot content of P, Cd, and Ge by percentages between 73% and 80% (significant only for Ge) and decreased shoot content of REET, Pb, and Cu by 28%, 35%, and 59%, respectively. For H. annuus grown on bioaugmented soil, shoot content of Ca, Cu, Ge, REET, and Pb increased by over 40%, with a negligible decrease observed for Cd. Summarily, results suggest that bioaugmentation with Bacillus amyloliquefaciens FZB42 could enhance biomass production, increase soil element bioavailability enhance, and increase or reduce plant accumulation of target elements. Additionally, differences in P use efficiency could influence bioaugmentation effects on P accumulation.

Endophytic Bacteria Colonizing the Petiole of the Desert Plant Zygophyllum dumosum Boiss: Possible Role in Mitigating Stress

Zygophyllum dumosum is a dominant shrub in the Negev Desert whose survival is accomplished by multiple mechanisms including abscission of leaflets to reduce whole plant transpiration while leaving the fleshy, wax-covered petioles alive but dormant during the dry season. Petioles that can survive for two full growing seasons maintain cell component integrity and resume metabolic activity at the beginning of the winter. This remarkable survival prompted us to investigate endophytic bacteria colonizing the internal tissues of the petiole and assess their role in stress tolerance. Twenty-one distinct endophytes were isolated by culturing from surface-sterile petioles and identified by sequencing of the 16S rDNA. Sequence alignments and the phylogenetic tree clustered the isolated endophytes into two phyla, Firmicutes and Actinobacteria. Most isolated endophytes displayed a relatively slow growth on nutrient agar, which was accelerated by adding petiole extracts. Metabolic analysis of selected endophytes showed several common metabolites whose level is affected by petiole extract in a species-dependent manner including phosphoric acid, pyroglutamic acid, and glutamic acid. Other metabolites appear to be endophyte-specific metabolites, such as proline and trehalose, which were implicated in stress tolerance. These results demonstrate the existence of multiple endophytic bacteria colonizing Z. dumosum petioles with the potential role in maintaining cell integrity and functionality via synthesis of multiple beneficial metabolites that mitigate stress and contribute to stress tolerance.

Impact of Soil Inoculation with Bacillus amyloliquefaciens FZB42 on the Phytoaccumulation of Germanium, Rare Earth Elements, and Potentially Toxic Elements

Bioaugmentation promises benefits for agricultural production as well as for remediation and phytomining approaches. Thus, this study investigated the effect of soil inoculation with the commercially available product RhizoVital^®42, which contains Bacillus amyloliquefaciens FZB42, on nutrient uptake and plant biomass production as well as on the phytoaccumulation of potentially toxic elements, germanium, and rare earth elements (REEs). Zea mays and Fagopyrum esculentum were selected as model plants, and after harvest, the element uptake was compared between plants grown on inoculated versus reference soil. The results indicate an enrichment of B. amyloliquefaciens in inoculated soils as well as no significant impact on the inherent bacterial community composition. For F. esculentum, inoculation increased the accumulation of most nutrients and As, Cu, Pb, Co, and REEs (significant for Ca, Cu, and Co with 40%, 2042%, and 383%, respectively), while it slightly decreased the uptake of Ge, Cr, and Fe. For Z. mays, soil inoculation decreased the accumulation of Cr, Pb, Co, Ge, and REEs (significant for Co with 57%) but showed an insignificant increased uptake of Cu, As, and nutrient elements. Summarily, the results suggest that bioaugmentation with B. amyloliquefaciens is safe and has the potential to enhance/reduce the phytoaccumulation of some elements and the effects of inoculation are plant specific.