Effect of bacterial inoculation of strains of Pseudomonas aeruginosa, Alcaligenes feacalis and Bacillus subtilis on germination, growth and heavy metal (Cd, Cr, and Ni) uptake of Brassica juncea

Two microbes assisting Miscanthus floridulus in remediating multi-metal(loid)s-contaminated soil

Miscanthus has good tolerance to multi-metal(loid)s and has received increasing attention in remediated studies of metal(loid)s-contaminated soil. In this study, we conducted phytoextraction techniques to investigate the synergic effects of remediation of multi-metal(loid)s-contaminated soil by Miscanthus floridulus (Lab.) and two plant growth-promoting bacteria (PGPB), TS8 and MR2, affiliated to Enterobacteriaceae. The results exhibited a decrease of arsenic (15.27-21.50%), cadmium (8.64-15.52%), plumbum (5.92-12.76%), and zinc (12.84-24.20%) except for copper contents in the soil in bacterial inoculation groups, indicating that MR2 and TS8 could enhance the remediation of metal(loid)s. Moreover, increased fresh/dry weight and height indicated that inoculated bacteria could promote Miscanthus growth. Although the activities of antioxidant enzymes and the content of chlorophyll in the overground tissues showed no significant increase or even decrease, the activities of antioxidant enzymes in the underground tissues and soil were elevated by 48.95-354.17%, available P by 19.07-23.02%, and available K by 15.34-17.79% (p < 0.05). Bacterial inoculants could also decrease the soil pH. High-throughput sequencing analysis showed that the bacterial inoculant affected the rhizosphere bacterial community and reduced community diversity, but the relative abundance of some PGPB was found to increase. Phylogenetic molecular ecological networks indicated that bacterial inoculants reduced interactions between rhizosphere bacteria and thereby led to a simpler network structure but increased the proportion of positive-correlation links and enhanced the metabiosis and symbiosis of those bacteria. Spearman's test showed that OTUs affiliated with Enterobacteriaceae and soil nutrients were critical for metal(loid) remediation and Miscanthus growth. The results of this study provide a basis for the synergic remediation of multi-metal(loid)s-contaminated soils by Miscanthus and PGPB and provide a reference for the subsequent regulation of Miscanthus remediation efficiency by the other PGPB or critical bacteria.

Isolation and identification of a new Bacillus glycinifermentans strain from date palm rhizosphere and its effect on barley seeds under heavy metal stress

Soil contamination by heavy metals is one of the major problems that adversely decrease plant growth and biomass production. Inoculation with the plant growth-promoting rhizobacteria (PGPR) can attenuate the toxicity of heavy metals and enhancing the plant growth. In this study, we evaluated the potential of a novel extremotolerant strain (IS-2 T) isolated from date palm rhizosphere to improve barley seedling growth under heavy metal stress. The species-level identification was carried out using morphological and biochemical methods combined with whole genome sequencing. The bacterial strain was then used in vitro for inoculating Hordeum vulgare L. exposed to three different Cr, Zn, and Ni concentrations (0.5, 1, and 2 mM) in petri dishes and different morphological parameters were assessed. The strain was identified as Bacillus glycinifermentans species. This strain showed high tolerance to pH (6-11), salt stress (0.2-2 M), and heavy metals. Indeed, the minimum inhibitory concentrations at which bacterium was unable to grow were 4 mM for nickel, 3 mM for zinc, more than 8 mM for copper, and 40 mM for chromium, respectively. It was observed that inoculation of Hordeum vulgare L. under metal stress conditions with Bacillus glycinifermentans IS-2 T stain improved considerably the growth parameters. The capacity of the IS-2 T strain to withstand a range of abiotic stresses and improve barley seedling development under lab conditions makes it a promising candidate for use as a PGPR in zinc, nickel, copper, and chromium bioremediation.

Mitigation of heavy metal stress in the soil through optimized interaction between plants and microbes

Agricultural as well as industrial processes, such as mining and textile activities, are just a few examples of anthropogenic activities that have a long-term negative impact on the environment. Each of the aforementioned factors increases the concentration of heavy metals in soil. Heavy metal contamination in soil causes a wide range of environmental issues and is harmful to microbes, plants, and animals. Because of their non-biodegradability and toxic effects, preventing additional metal contamination and remediating the vast majority of contaminated sites around the world is critical. Hence, this review focuses on the effects of metal contamination on soil microbes, as well as plant-microbe interactions. Plant-associated probiotics reduce metal accumulation; the introduction of beneficial microbes is regarded as one of the most promising approaches to improving metal stress tolerance; thus, the study focuses on plant-microbe interactions as well as their actual implications via phytoremediation. Plant-microbe interaction can play an important role in acclimating vegetation (plants) to metalliferous conditions and should thus be studied to improve microbe-aided metal tolerance in plants. Plant-interacted microbes reduce metal accumulation in plant cells and metal bioaccumulation in the soil through a variety of processes. A novel phytobacterial approach, such as genetically modified microbes, is now being used to improve heavy metal cleanup as well as stress tolerance among plants. This review examines our current understanding of such negative consequences of heavy metal stresses, signaling responses, and the role of plant-associated microbiota in heavy metal stress tolerance and interaction.

Evaluating the potential of Bacillus licheniformis YZCUO202005 isolated from lichens in maize growth promotion and biocontrol

Lichens exist in an organismal organization of mycobiont, photobiont, and non-photoautotrophic bacteria. These organisms contribute to the growth of lichens even in poor nutrition substrates. However, studies on the isolation and application of non-photoautotrophic bacteria in plant growth and biocontrol are scanty. Therefore, a study was conducted to isolate and evaluate the potential of non-photoautotrophic bacteria from lichen tissues in maize plant growth promotion and biocontrol of plant pathogens (fungi and bacteria). Five bacterial strains were isolated and tested for their ability to produce indole-3-Acetic Acid (IAA). One bacterium named YZCUO202005 produced IAA, siderophores and biofilms, solubilized phosphate and potassium and exhibited extracellular enzymes (cellulases, proteases, amylase, and β -1,3-Glucanase). Based on the 16S rRNA sequence analysis results, YZCUO202005 was identified as Bacillus licheniformis. The strain inhibited the growth of five pathogenic fungi with an inhibition percent of between 58.7% and 71.7% and two pathogenic bacteria. Under greenhouse conditions, YZCUO202005 was tested for its abilities to enhance maize seed germination, and vegetative growth. Compared with the control treatment, the strain significantly enhanced the growth of stem length (i.e. 18 ± 0.64 cm, 78 ± 0.92 cm), leaf length (i.e. 10 ± 0.36 cm, 57 ± 1.42 cm), leaf chlorophyll levels (i.e., 13 ± 0.40, 40 ± 0.43 SPAD), and root length (i.e, 9.8 ± 2.25 cm, 22.5 ± 6.59 cm). Our results demonstrated that B. licheniformis YZCUO202005 from lichens has the potential to promote plant growth and reduce fungal and bacterial pathogens' growth. Furthermore, the results suggest that lichens are naturally rich sources of plant growth promotion and biocontrol agents that would be used in agriculture.

Comparative Genomics Reveals Novel Species and Insights into the Biotechnological Potential, Virulence, and Resistance of Alcaligenes

Alcaligenes is a cosmopolitan bacterial genus that exhibits diverse properties which are beneficial to plants. However, the genomic versatility of Alcaligenes has also been associated with the ability to cause opportunistic infections in humans, raising concerns about the safety of these microorganisms in biotechnological applications. Here, we report an in-depth comparative analysis of Alcaligenes species using all publicly available genomes to investigate genes associated with species, biotechnological potential, virulence, and resistance to multiple antibiotics. Phylogenomic analysis revealed that Alcaligenes consists of at least seven species, including three novel species. Pan-GWAS analysis uncovered 389 species-associated genes, including cold shock proteins (e.g., cspA) and aquaporins (e.g., aqpZ) found exclusively in the water-isolated species, Alcaligenes aquatilis. Functional annotation of plant-growth-promoting traits revealed enrichment of genes for auxin biosynthesis, siderophores, and organic acids. Genes involved in xenobiotic degradation and toxic metal tolerance were also identified. Virulome and resistome profiles provide insights into selective pressures exerted in clinical settings. Taken together, the results presented here provide the grounds for more detailed clinical and ecological studies of the genus Alcaligenes.

Role of Candida in the bioremediation of pollutants: a review

The population and modernization of society have increased dramatically from past few decades. In order to meet societal expectations, there has been a massive industrialization and resource exploitation. Anthropogenic practices like disposal of hazardous waste, large carbon footprint release variety of xenobiotic substances into the environment, which endanger the health of the natural ecosystem. Therefore, discovering proper long-term treatment approaches is a global concern. Various physical and chemical approaches are employed to remove contaminants. However, these technologies possess limitations like high cost and low efficacy. Consequently, bioremediation is regarded as one of the most promising remedies to these problems. It creates the option of either totally removing pollutants or transforming them into nonhazardous compounds with the use of natural biological agents. Several microorganisms are being utilized for bioremediation among which yeasts possess benefits such as high biodegradability, ease of cultivation etc. The yeast of Candida genus has the capability to effectively eliminate heavy metal ions, as well as to degrade and emulsify hydrocarbons which makes it a promising candidate for this purpose. The review highlights many potential uses of Candida in various remediation strategies and discusses future directions for research in this field.

Biofilm-forming plant growth-promoting rhizobacterial consortia isolated from mines and dumpsites assist green remediation of toxic metal (Ni and Pb) using Brassica juncea

To study how biofilm-forming rhizobacteria isolated from mines and dumpsites improved the phytoremediation efficacy of B. juncea in metal-contaminated soil. Out of 91 isolates, six were chosen for research based on their tolerance to metals, and their efficient PGPR properties, and subjected to the design of a consortium. A compatibility study revealed no antagonistic interaction between rhizobacterial-consortiums. The results of the biofilm formation and FEG-SEM studies revealed that a consortium-BC8 formed a strong biofilm on the root surface of B. juncea seedlings. Based on results obtained with the phytoextraction efficiency of B. juncea in consortium-BC8 (SMHMZ46 and SMHMP23), they were identified as Klebsiella variicola and Pseudomonas otitidis, respectively, and submitted to NCBI GenBank with accession numbers MZ145092 and OK560623. This rhizobacteria is the first to be reported as assisting Ni and Pb phytoremediation by employing B. juncea. Soil inoculation with consortium-BC8 increased the amount of soluble Ni and Pb by 13.25-fold and 10.69-fold, respectively, when compared to the control. These consortiums-BC8 significantly increased vegetative growth and metal accumulation in root and shoot with a translocation-factor of 1.58 for Ni and soil to root with a bioconcentration-factor of 1.3 for Pb in B. juncea grown in individual soil contamination with 96.05 mg/kg NiCl2 and 89.63 mg/kg Pb(NO3)2, which are significantly higher than other consortium treatments and the non-inoculated control. B. juncea amendments with a biofilm-forming consortium-BC8 having TF, BCF, and BAC > 1 for Ni, whereas BCF > 1, TF, and BAC < 1 for Pb, are appropriate for green remediation of Ni and phytostabilization of Pb.

Plant growth-promoting and heavy metal-resistant Priestia and Bacillus strains associated with pioneer plants from mine tailings

Open mine tailings dams are extreme artificial environments containing sizeable potentially toxic elements (PTEs), including heavy metals (HMs), transition metals, and metalloids. Furthermore, these tailings have nutritional deficiencies, including assimilable phosphorus sources, organic carbon, and combined nitrogen, preventing plant colonization. Bacteria, that colonize these environments, have mechanisms to tolerate the selective pressures of PTEs. In this work, several Priestia megaterium (formerly Bacillus megaterium), Bacillus mojavensis, and Bacillus subtilis strains were isolated from bulk tailings, anthills, rhizosphere, and endosphere of pioneer plants from abandoned mine tailings in Zacatecas, Mexico. Bacillus spp. tolerated moderate HMs concentrations, produced siderophores and indole-3-acetic acid (IAA), solubilized phosphates, and reduced acetylene in the presence of HMs. The strains harbored different PIB-type ATPase genes encoding for efflux pumps and Cation Diffusion Facilitator (CDF) genes. Moreover, nifH and nifD nitrogenase genes were detected in P. megaterium and B. mojavensis genomic DNA. They showed similarity with sequences of the beta-Proteobacteria species, which may represent likely horizontal transfer events. These Bacillus species precede the colonization of mine tailings by plants. Their phenotypic and genotypic features could be essential in the natural recovery of the sites by reducing the oxidative stress of HMs, fixing nitrogen, solubilizing phosphate, and accumulating organic carbon. These traits of the strains reflect the adaptations of Bacillus species to the mine tailings environment and could contribute to the success of phytoremediation efforts.

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

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

Chlorella sorokiniana FK-montmorillonite interaction enhanced remediation of heavy metals in tailings

Non-ferrous metal mining activities are known to cause ecological irreversible damage in the tailings and surrounding areas as well as heavy metal (HM) contamination. The enhancement of Chlorella-montmorillonite interaction on the remediation of HM contaminated tailings was verified from the lab to the tailings in Daye City, Hubei Province, China. The results showed a positive correlation between the quantity of montmorillonite and the transformation of Pb and Cu into residual and carbonate-binding states, which resulted in a considerable decrease in the leaching ratio. The buildup of tailings fertility throughout this process benefited from montmorillonite's ability to buffer environmental changes and store water. This further offers a required environmental foundation for the rebuilding of microbial community and the growth of herbaceous plants. The structural equation model demonstrated that the interaction between Chlorella and montmorillonite directly affected the stability of HM, and that this interaction also had an impact on the accumulation of organic carbon, total nitrogen, and available phosphorus, which improved the immobilization of Pb, Cu, Cd, and Zn. This work made the first attempt to apply Chlorella-montmorillonite composite to in-situ tailings remediation, and proposed that the combination of inorganic clay minerals and organic microorganisms was an eco-friendly, long-lasting, and efficient method for immobilizing multiple-HMs in mining areas.

Bioaccumulation and Bioremediation of Heavy Metals in Fishes-A Review

Heavy metals, the most potent contaminants of the environment, are discharged into the aquatic ecosystems through the effluents of several industries, resulting in serious aquatic pollution. This type of severe heavy metal contamination in aquaculture systems has attracted great attention throughout the world. These toxic heavy metals are transmitted into the food chain through their bioaccumulation in different tissues of aquatic species and have aroused serious public health concerns. Heavy metal toxicity negatively affects the growth, reproduction, and physiology of fish, which is threatening the sustainable development of the aquaculture sector. Recently, several techniques, such as adsorption, physio-biochemical, molecular, and phytoremediation mechanisms have been successfully applied to reduce the toxicants in the environment. Microorganisms, especially several bacterial species, play a key role in this bioremediation process. In this context, the present review summarizes the bioaccumulation of different heavy metals into fishes, their toxic effects, and possible bioremediation techniques to protect the fishes from heavy metal contamination. Additionally, this paper discusses existing strategies to bioremediate heavy metals from aquatic ecosystems and the scope of genetic and molecular approaches for the effective bioremediation of heavy metals.

Mercury remediation potential of mercury-resistant strain Rheinheimera metallidurans sp. nov. isolated from a municipal waste dumping site

A novel mercury-resistant bacterium, designated strain DCL_24^T, was isolated from the legacy waste at the Daddu Majra dumping site in Chandigarh, India. It showed resistance up to 300 µM of inorganic mercury (mercuric chloride). The isolate was found to be a Gram-negative, facultative anaerobic, motile, and rod-shaped bacterium that can grow at 4 - 30 °C (optimum 25 °C), pH 6.0 - 12.0 (optimum 7.0), and 0 - 4.0 % (w/v) NaCl (optimum 0.5 - 2.0 %). The 16 S rRNA gene-based phylogenetic analysis showed that DCL_ 24 ^T shared a 97.53 % similarity with itsºlosest type strain Rheinheimera muenzenbergensis E-49^T. Insilico DNA-DNA hybridization and average nucleotide identity values were found to be 18.60 % and 73.77 %, respectively, between the genomes of DCL_24^T and R. muenzenbergensis E-49^T. The strain DCL_24^T has 44.33 DNA G+C content (mol %). Based on the phenotypic, chemotaxonomic, and genotypic data, the strain DCL_24^T represents a novel species within the genus Rheinheimera, for which the name Rheinheimera metallidurans sp. nov is proposed. The type strain is DCL_24^T (MTCC13203^T = NBRC115780^T = JCM 35551 ^T). The isolate was found to volatilize and remove mercury efficiently, as demonstrated by X-ray film and dithizone-based colorimetric methods. Around 92 % of mercury removal was observed within 48 h. The mercury-resistant determinant mer operon consisting of merA, encoding the mercuric reductase enzyme, and transport and regulatory genes (merT, merP, merD, and merR) were found in the isolate. Relative expression analysis of merA at increasing concentrations of HgCl₂ was confirmed by quantitative real-time PCR. These data indicate the merA-mediated reduction of toxic Hg²⁺ into a non-toxic volatile Hg⁰. The phytotoxicity assay performed using Arabidopsis thaliana seeds further demonstrated the mercury toxicity reduction potential of DCL_24^T. The study shows that this novel isolate, DCL_24^T, is an interesting candidate for mercury bioremediation. However, further studies are required to assess the bioremediation efficacy of the strain under the harsh environmental conditions prevailing in polluted sites.

Devosia oryzisoli sp. nov., a novel moderately halotolerant bacterium isolated from the roots of rice plants and genome mining revealed the biosynthesis potential as plant growth promoter

A Gram-stain-negative, halotolerant bacterium designated as PTR5^T was isolated from the roots of rice plants, collected in Ilsan, South Korea. Cells were, aerobic, asporogenous, motile, rod-shaped, white in color, and grew at 5-38 °C (optimum 30 °C), at pH 5.0-0-8.0 (optimum, 7.0) and tolerates up to 10% (w/v) NaCl (optimum, 0% NaCl). According to the EZbioCloud server the most closely related Devosia species to strain PTR5^T based on 16 S rRNA gene sequence comparison are Devosia crocina (97.4%), followed by D. soli (97.2%), D. lucknowensis (96.9%) and D. marina (96.5%). The respiratory quinone was identified as Q-10. The major polar lipids were phosphatidylglycerol and diphosphatidylglycerol. C_16:0, C_18:1 ω7c 11-methyl and summed feature 8 (comprising C_18:1 ω7c/C_18:1 ω6c) constituted the main cellular fatty acids. The draft genome sequence of strain PTR5^T was 3,689,283 bp in size. The average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH) and amino acid identity (AAI) values between strain PTR5^T and its close relative were 72.8-76.8%, 19-20.7% and 70.3-75%, respectively. The G + C content was 63.7%. Strain PTR5^T was able to produce siderophore and indole acetic acid (IAA) in the presence of L-tryptophan. Genes for siderophore production, auxin responsive and tryptophan biosynthesis were present in the genome of novel strain. Also, gene clusters involved in detoxification of various metal pollutants and antibiotics were also revealed in the genome of novel strain PTR5^T, this suggest that novel strain can facilitate bioremediation of heavy metals and antibiotics in contaminated areas. This study aimed to determine the detailed taxonomic position of the strain PTR5^T using the modern polyphasic approach. On the basis of evidence presented in this study, strain PTR5^T is considered to represent a novel species of the genus Devosia, for which the name Devosia oryzisoli sp. nov. (type strain PTR5^T (KCTC 82691^T = TBRC 15163^T) is proposed.

Chromium toxicity, speciation, and remediation strategies in soil-plant interface: A critical review

In recent decades, environmental pollution with chromium (Cr) has gained significant attention. Although chromium (Cr) can exist in a variety of different oxidation states and is a polyvalent element, only trivalent chromium [Cr(III)] and hexavalent chromium [Cr(VI)] are found frequently in the natural environment. In the current review, we summarize the biogeochemical procedures that regulate Cr(VI) mobilization, accumulation, bioavailability, toxicity in soils, and probable risks to ecosystem are also highlighted. Plants growing in Cr(VI)-contaminated soils show reduced growth and development with lower agricultural production and quality. Furthermore, Cr(VI) exposure causes oxidative stress due to the production of free radicals which modifies plant morpho-physiological and biochemical processes at tissue and cellular levels. However, plants may develop extensive cellular and physiological defensive mechanisms in response to Cr(VI) toxicity to ensure their survival. To cope with Cr(VI) toxicity, plants either avoid absorbing Cr(VI) from the soil or turn on the detoxifying mechanism, which involves producing antioxidants (both enzymatic and non-enzymatic) for scavenging of reactive oxygen species (ROS). Moreover, this review also highlights recent knowledge of remediation approaches i.e., bioremediation/phytoremediation, or remediation by using microbes exogenous use of organic amendments (biochar, manure, and compost), and nano-remediation supplements, which significantly remediate Cr(VI)-contaminated soil/water and lessen possible health and environmental challenges. Future research needs and knowledge gaps are also covered. The review's observations should aid in the development of creative and useful methods for limiting Cr(VI) bioavailability, toxicity and sustainably managing Cr(VI)-polluted soils/water, by clear understanding of mechanistic basis of Cr(VI) toxicity, signaling pathways, and tolerance mechanisms; hence reducing its hazards to the environment.

Microbial seed coating: An attractive tool for sustainable agriculture

Seed coating is considered one of the best methods to promote sustainable agriculture where the physical and physiological properties of seeds can be improved to facilitate planting, increase growth indices and alleviate abiotic and biotic stresses. Several methods of seed coating are used to attain good application uniformity and adherence in the seed coating process. Seed coating has been tested in seeds of various plant species with different dimensions, forms, textures, and germination types. Plant beneficial microorganisms (PBM), such as rhizobia, bacteria, and fungi inoculated via seed inoculation can increase seed germination, plant performance and tolerance across biotic (e.g., pathogens and pests) and abiotic stress (e.g., salt, drought, and heavy metals) while reducing the use of agrochemical inputs. In this review, the microbial seed coating process and their ability to increase seed performance and protect plants from biotic and abiotic stresses are well discussed and highlighted in sustainable agricultural systems.

The Mechanism of Cu2+ Sorption by Rice Straw Biochar and Its Sorption-Desorption Capacity to Cu2+ in Soil

Copper (Cu) pollution in soils has received considerable research attention globally, and biochar has been widely used as an adsorbent for soil pollution of Cu. However, most of the studies focused on the adsorption capacity of biochar, the bioavailability of Cu absorbed by biochar remains unclear. In this work, rice straw biomass was pyrolyzed under oxygen-limited conditions at 400°C (BC400) and 600°C (BC600), their apparent structure, group characteristics, and basic physical and chemical properties were determined. The isothermal and kinetics adsorption of Cu by BC400 and BC600 were analyzed. A pot experiment was used to evaluate the passivation of Cu in the soil by biochar and the bioavailability of Cu adsorbed by biochar in the soil. The smooth surfaces of BC400 evolved into more rough surfaces for BC600, and both types of surfaces may give active sorption sites for Cu, according to SEM pictures. FTIR analysis suggested that BC600 is endowed with more condensed aromatic carbon structures and more available polar functional groups. The adsorption processes of Cu²⁺ by biochar were better fitted Langmuir equation and pseudo-second-order kinetic model. The adsorption isotherms showed monolayer adsorption of Cu²⁺ on biochar. The maximum adsorption capacities of BC600 and BC400 on Cu²⁺ were 43.75 and 30.70 mg g^-1, respectively. Moreover, the pot experiment showed that BC400 and BC600 not only have a strong "passivation" effect on Cu in soil but also prevent the release of adsorbed Cu. Overall, more aromatic carbon structure, more polar functional groups, and higher pH are associated with BC600's increased Cu immobilization ability in soil.

Soil bacteria around a derelict tailings pile with different metal pollution gradients: community composition, metal tolerance and influencing factors

Bacteria play a vital role in ecological processes of soil contaminated by heavy metals. Here, soil sampling was carried out around a tailings pile contaminated to different degrees by cadmium (Cd), lead (Pb) and arsenic (As). The bacteria in the soil were cultured, separated and purified on Luria-Bertani medium, and the changes in bacterial communities in soils with different pollution levels were analysed with 16S rRNA sequencing. Bacillus pacificus strain MZ520364 was found to be highly tolerant to Cd, Pb and As, and single-metal and multimetal tolerance experiments were further conducted with this strain. The results obtained from alpha diversity and operational taxonomic unit (OTU) statistical analyses showed a significant difference in bacterial composition among soils with different metal pollution levels, and the highest bacterial diversity was found at the most severely polluted site. Evidence from variance partitioning analysis (VPA) and the Spearman correlation heatmap analysis showed that the leading factors affecting bacterial community composition were cation exchange content (CEC), pH, total Zn, total As, and available As concentrations in soil. Additionally, in the single-metal treatments, B. pacificus MZ520364 could tolerate 600 mg/L Cd²⁺, 1000 mg/L Pb²⁺ or 700 mg/L As³⁺. When Cd, Pb and As coexisted, the best growth of B. pacificus MZ520364 was present at 120 mg/L Cd²⁺, 200 mg/L Pb²⁺ and 150 mg/L As³⁺. The effect of Cd, Pb and As on the growth of the strain followed the order of Cd > As > Pb, and the heavy metal combination showed more toxicity than single metals. In summary, our results revealed the ecological impact of soil physicochemical properties on the diversity and richness of soil bacterial communities and suggested that B. pacificus MZ520364 may be used for the remediation of Cd-Pb-As co-contaminated soil.

Diversity and composition of soil bacteria between abandoned and selective-farming farmlands in an antimony mining area

Background and aims

Land abandonment and selective farming are two common management methods to restore the soil conditions of low-pollution farmland in mining areas. The soil bacterial community plays an important role in farmland soil restoration; however, few studies have compared the composition and diversity of soil bacteria between the abandoned farmlands (AFS) and selective-farming farmlands (FFS). Here, the effects of AFS and FFS on soil properties and bacterial diversity were evaluated in an antimony (Sb) mining area in southern China. This study aimed to identify effective land management methods in terms of positive or negative changes in soil environment and bacterial diversity.

Methods

16S rRNA high-throughput sequencing was used to compare the diversity and composition of soil bacteria between AFS and FFS in the Xikuangshan (the largest Sb mine in the world).

Results

Compared to AFS, FFS had higher Sb concentration and nutritional properties (e.g., available N, P, and K) and lower Zn concentration (p < 0.05). The bacterial alpha diversity including Chao1 index, Simpson index, Shannon index and Pielou₋e index in FFS was higher than AFS (p < 0.05). At the phylum level, FFS had higher relative abundances of Chloroflexi, Acidobacteria, Gemmatimonadetes, and Rokubacteria, and lower relative abundances of Firmicutes, Actinobacteria, and Bacteroidetes. At the genus level, FFS had higher relative abundances of Acidothermus, Haliangium, and Rokubacteriales, and lower relative abundances of Bacillus, Rhodococcus, Sphingomonas, and 67-14. Redundancy analysis indicated that soil heavy metal content and soil fertility were closely correlated with the soil bacterial community. Altogether, selective farming of low-pollution farmland in the mining area can improve soil properties and soil bacterial diversity.

Plant growth-promoting rhizobacteria for orphan legume production: Focus on yield and disease resistance in Bambara groundnut

Orphan legumes are now experiencing growing demand due to the constraints on available major food crops. However, due to focus on major food crops, little research has been conducted on orphan legumes compared to major food crops, especially in microbiome application to improve growth and yield. Recent developments have demonstrated the enormous potential of beneficial microbes in growth promotion and resistance to stress and diseases. Hence, the focus of this perspective is to examine the potential of plant growth promoting rhizobacteria (PGPR) to improve Bambara groundnut yield and quality. Further insights into the potential use of PGPR as a biological control agent in the crop are discussed. Finally, three PGPR genera commonly associated with plant growth and disease resistance (Bacillus, Pseudomonas, and Streptomyces) were highlighted as case studies for the growth promotion and disease control in BGN production.

Phylogenetic Illustration of Eisenia fetida Associated Vermi-bacteria Involved in Heavy Metals Remediation and Retaining Plant Growth Promoting Traits

Heavy metals contamination in the soil is a major threat to wildlife, the environment, and human health. Microbial remediation is an emerging and promising technology to reduce heavy metals toxicity. Therefore, the present research aimed to isolate and to identify the heavy metals tolerated bacteria from the Eisenia fetida for the first time, and to screen the bacto-remediation capabilities and plant growth promoting traits of vermi-bacterial isolates. Vermi-bacteria was isolated from the gut of E. fetida, identified through staining, culturing, biochemical tests, and ribotyping. Plant growth-promoting traits were also evaluated. Phylogenetic results revealed that isolated Vermi-bacterial strains showed resemblance with Bacillus thuringiensis, Bacillus aryabhattai, Staphylococcus hominis, Bacillus toyonensis, Bacillus cabrialesii, Bacillus tequilensis, Bacillus mojavensis, Bacillus amyloliquefaciens, Bacillus toyonensis, Bacillus anthracis, and Bacillus paranthracis. All identified Vermi-bacterial species are Gram-positive (rod and cocci) in nature, not only indicated the efficient biosorption of lead, cadmium, and chromium but also produce all plant growth stimulating traits such as indole acetic acid (IAA), amylase, protease, lipase, hydrogen cyanide, ammonia, and siderophore production, and also act as a phosphate solubilizers. Bacillus anthracis showed significant production of siderophore (33.0±0.0 mm), phosphate solubilizing (33.0±0.0 mm), proteolytic (15.0±0.0 mm), and lipolytic activities (20.0±0.0 mm) compared to other vermi-bacterial isolates. Bioaccumulation factor results revealed that Bacillus anthracis showed more accumulation of Cd (12.00±0.01 ppm), Cr (5.38±0.01 ppm), and Pb (4.38±0.01 ppm). Therefore, the current findings showed that all identified vermi-bacteria could be used as potential bactoremediation agents in heavy metals polluted environments and could be used as microbial biofertilizers to enhance crop production in a polluted area.

Sustainable Intensification of Maize in the Industrial Revolution: Potential of Nitrifying Bacteria and Archaea

Sustainable intensification is a means that proffer a solution to the increasing demand for food without degrading agricultural land. Maize is one of the most important crops in the industrial revolution era, there is a need for its sustainable intensification. This review discusses the role of maize in the industrial revolution, progress toward sustainable production, and the potential of nitrifying bacteria and archaea to achieve sustainable intensification. The era of the industrial revolution (IR) uses biotechnology which has proven to be the most environmentally friendly choice to improve crop yield and nutrients. Scientific research and the global economy have benefited from maize and maize products which are vast. Research on plant growth-promoting microorganisms is on the increase. One of the ways they carry out their function is by assisting in the cycling of geochemical, thus making nutrients available for plant growth. Nitrifying bacteria and archaea are the engineers of the nitrification process that produce nitrogen in forms accessible to plants. They have been identified in the rhizosphere of many crops, including maize, and have been used as biofertilizers. This study's findings could help in the development of microbial inoculum, which could be used to replace synthetic fertilizer and achieve sustainable intensification of maize production during the industrial revolution.

Pseudomonas sp. TCd-1 significantly alters the rhizosphere bacterial community of rice in Cd contaminated paddy field

Cadmium (Cd) pollution of paddy soils is one of the main concerns causing food security and environmental problems. Microbial bioremediation is an effective and eco-friendly measure that uses microbes to reduce Cd accumulation in crops. Additionally, rhizosphere bacterial communities also act essential roles in crop tolerance of heavy metals. However, the effects of inoculations with Cd resistant bacteria on crop rhizosphere bacterial communities under Cd exposure are largely unknown. In this study, we used high-throughput 16S rRNA gene sequencing technologies to explore the community structure and co-occurrence network of the rhizosphere bacterial communities associated with the rice crop under different Cd treatments and the application of Cd-tolerant strain Pseudomonas sp. TCd-1. We found that the strain TCd-1 both significantly reduced the rhizobacterial alpha diversity and changed the beta diversity. PERMANOVA and NMDS analysis showed that Cd stress and TCd-1 strain could act as strong environmental filters resulting in observable differentiation of rhizobacterial community composition among different groups. In addition, RDA results indicated that the rhizosphere pH, root Cd content, catalase (CAT), urease (URE), gibberellic acid (GA3) exert significant association with rhizosphere bacterial assembly. PICRUSt analysis revealed that the TCd-1 strain improved the metabolic capacity of rhizosphere bacteria under Cd stress. Furthermore, co-occurrence network topological features and keystone taxa also varied among different groups. This study could provide necessary insights into developing an efficient bioremediation and safe production of rice crops in Cd contaminated paddy fields with the application of Pseudomonas sp. TCd-1 strain, as well as advance our understanding of the principles of rhizosphere bacterial community assembly under Cd stress.

Bacillus subtilis Impact on Plant Growth, Soil Health and Environment: Dr. Jekyll and Mr. Hyde

The increased dependence of farmers on chemical fertilizers poses a risk to soil fertility and ecosystem stability. Plant growth-promoting rhizobacteria (PGPR) are at the forefront of sustainable agriculture, providing multiple benefits for the enhancement of crop production and soil health. Bacillus subtilis is a common PGPR in soil that plays a key role in conferring biotic and abiotic stress tolerance to plants by induced systemic resistance (ISR), biofilm formation, and lipopeptide production. As a part of bioremediating technologies, Bacillus spp. can purify metal contaminated soil. It acts as a potent denitrifying agent in agroecosystems while improving the carbon sequestration process when applied in a regulated concentration. Although it harbors several antibiotic resistance genes (ARGs), it can reduce the horizontal transfer of ARGs during manure composting by modifying the genetic makeup of existing microbiota. In some instances, it affects the beneficial microbes of the rhizosphere. External inoculation of B. subtilis has both positive and negative impacts on the endophytic and semi-synthetic microbial community. Soil texture, type, pH, and bacterial concentration play a crucial role in the regulation of all these processes. Soil amendments and microbial consortia of Bacillus produced by microbial engineering could be used to lessen the negative effect on soil microbial diversity. The complex plant-microbe interactions could be decoded using transcriptomics, proteomics, metabolomics, and epigenomics strategies which would be beneficial for both crop productivity and the well-being of soil microbiota. Bacillus subtilis has more positive attributes similar to the character of Dr. Jekyll and some negative attributes on plant growth, soil health, and the environment akin to the character of Mr. Hyde.

Changes in microbial community diversity, composition, and functions upon nitrate and Cr(VI) contaminated groundwater

With the increasing occurrences of nitrate and Cr(VI) pollution globally, microbially driven pollutant reduction and its interaction effects were of growing interest. Despite the increasing number of experimental reports on the simultaneous reduction of nitrate and Cr(VI), a broad picture of the keystone species and metabolic differences in this process remained elusive. This study explored the changing of microorganisms with the introduction of Cr(VI)/NO₃^- through analyzing 242 samples from the NCBI database. The correlation between microbial abundance and environmental factors showed that, the types of energy substances and pollutants species in the environment had an impact on the diversity of microorganisms and community structure. The genus of Zoogloea, Candidatus Accumulibacter, and Candidatus Kapabacteria sp. 59-99 had the ability of denitrification, while genus of Alcaligenes, Kerstersia, Petrimonas, and Leucobacter showed effectively Cr(VI) resistance and reducing ability. Azoarcus, Pseudomonas, and Thauera were recognized as important candidates in the simultaneous reduction of nitrate and Cr(VI). Metagenomic predictions of these microorganisms using PICRUSt2 further highlighted the enrichment of Cr(VI)and nitrate reduction-related genes (such as chrA and norC). Special attention should therefore be paid to these bacteria in subsequent studies to evaluate their performance and mechanisms involved in simultaneous denitrification and chromium removal. The microbial co-occurrence network analysis conducted on this basis emphasized a strong association between community collaboration and pollution removal. Collectively, either site surveys or laboratory experiments, subsequent studies should focus on these microbial populations and the interspecific collaborations as they strongly influence the occurrence of simultaneous nitrate and Cr(VI) reduction.

Enhanced remediation of pollutants by microorganisms-plant combination

The pollutants have become ubiquitous in the total environment (water, soil and air) due to human activities and they are hazardous to all forms of life on the earth. This problem has made scientists focus on mitigating or complete reduction in pollutants by several means. Microorganism and plants are known to scavenge pollutants. Both are studied enormously in reducing, refining, and removing pollutants from the environment successfully. But, their slow process for removal is disadvantage. However, according to recent advancements in the abatement of pollutants, a combined system of both microorganisms and plant has shown to enhance the remediation of pollutants to an efficient level. In a nutrient-depleted pollutant-rich environment, when suitable plant and microorganisms are introduced, the plant interacts with the rhizosphere and root associate with microorganisms to survive in toxic conditions. The chemicals released by plants signal the microorganisms for interactions. This interaction leads in higher germination efficiency and enhanced root elongation which results in enhanced degradation of pollutants in both rhizosphere and phyllosphere. In this background, the current review article provides an overview of the recent advancement in microorganisms plant combined systems in enhanced removal of several recalcitrant pollutants. The conclusion highlights the challenges and future perspectives in this area of research.

Isolation, characterization, and evaluation of a high-siderophore-yielding bacterium from heavy metal-contaminated soil

Heavy metal-resistant siderophore-producing bacteria (SPB) with plant growth-promoting traits can assist in phytoremediation of heavy metal-contaminated soil. We isolated siderophore-producing bacteria from Pb and Zn mine soil in Shangyu, Zhejiang, China. The isolate with the highest siderophore production, strain SX9, was identified as Burkholderia sp. Burkholderia sp. SX9 produced catecholate-type siderophore, with the highest production at a pH range of 6.0 to 8.0, a temperature range of 20 to 30 °C and NaCl concentration below 2%. Siderophore production was highest without Fe³⁺ and became gradually lower with increasing Fe³⁺ concentration. Minimal inhibitory concentrations (MIC) of Pb²⁺, Zn²⁺, Cu²⁺, and Cd²⁺ were 4000, 22000, 5000, and 2000 μmol L^-1, respectively. The strain had a strong metal solubilization ability: the contents of Cu²⁺, Zn²⁺, and Cd²⁺ in the supernatant were 47.4%, 133.0%, and 35.4% higher, respectively, in strain SX9-inoculated cultures than in the not inoculated controls. The siderophore produced by strain SX9 could combine with Fe³⁺, Zn²⁺, and Cd²⁺ with good effectiveness. The plant growth-promoting traits of the strain included indole acetic acid (IAA) production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, and phosphate solubilization capability. Compared to the uninoculated growth medium and SX9 culture supernatant, the germination rate of Lolium perenne seeds was higher when inoculated with strain SX9 culture. In the experiment of seed germination, adding bacterial culture or supernatant could alleviate the toxicity of heavy metals to L. perenne seed germination. Under Cu²⁺ and Zn²⁺ stress, strain SX9 promoted the germination rate. Taken together, Burkholderia sp. SX9 had properties beneficial in the microbial enhancement of phytoremediation of soil contaminated with heavy metals.

Recent Developments in Microbe-Plant-Based Bioremediation for Tackling Heavy Metal-Polluted Soils

Soil contamination with heavy metals (HMs) is a serious concern for the developing world due to its non-biodegradability and significant potential to damage the ecosystem and associated services. Rapid industrialization and activities such as mining, manufacturing, and construction are generating a huge quantity of toxic waste which causes environmental hazards. There are various traditional physicochemical techniques such as electro-remediation, immobilization, stabilization, and chemical reduction to clean the contaminants from the soil. However, these methods require high energy, trained manpower, and hazardous chemicals make these techniques costly and non-environment friendly. Bioremediation, which includes microorganism-based, plant-based, microorganism-plant associated, and other innovative methods, is employed to restore the contaminated soils. This review covers some new aspects and dimensions of bioremediation of heavy metal-polluted soils. The bioremediation potential of bacteria and fungi individually and in association with plants has been reviewed and critically examined. It is reported that microbes such as Pseudomonas spp., Bacillus spp., and Aspergillus spp., have high metal tolerance, and bioremediation potential up to 98% both individually and when associated with plants such as Trifolium repens, Helianthus annuus, and Vallisneria denseserrulata. The mechanism of microbe's detoxification of metals depends upon various aspects which include the internal structure, cell surface properties of microorganisms, and the surrounding environmental conditions have been covered. Further, factors affecting the bioremediation efficiency and their possible solution, along with challenges and future prospects, are also discussed.

Changes in diversity and composition of rhizosphere bacterial community during natural restoration stages in antimony mine

Background

Open pit antimony (Sb) mining causes serious soil pollution, and phytoremediation is a low-cost approach to remediate heavy metal contaminated soil. Rhizosphere bacteria play an important role in ecological restoration in mining areas. There is a knowledge gap on how to find suitable rhizosphere microorganisms to improve the phytoremediation effect. Understanding the differences of rhizosphere bacterial diversity in different restoration stages is helpful to find suitable bacteria for ecological restoration.

Methods

A method of the substitution of "space" for "time" was used to study the effect of natural restoration on rhizosphere bacterial community. According to the dominant vegetation types (herb, shrub, and tree) in the natural restoration area of Sb mining, the early restoration (ER), middle restoration (MR), and later restoration (LR) from the largest Sb mine (Xikuangshan mine) in the world were selected to evaluate the differences in the composition and diversity of rhizosphere bacteria during three natural restoration stages. Each restoration stage had five samples. To determine the relationship between restoration stages and bacterial diversity in the rhizosphere, high throughput sequencing of PCR amplified were used.

Results

Alpha diversity, as assessed by Chao indices, appeared lowest in ER but this trend was not seen with other diversity metrics, including the Simpson and Shannon. Beta diversity analysis suggested there were differences in rhizobacterial community structure associate with restoration stage. At the phylum level, natural restoration led to a significant increase in the relative abundance of Actinobacteria in the MR, and a significant decrease in the relative abundance of Patescibacteria in the LR. Additionally, Calditrichaeota, Deferribacteres and Epsilonbacteraeota were only found in ER. At the genus level, the relative abundance of RB41 and Haliangium were highest in LR plots, while that of Bacillus and Gaiella were highest in ER plots. Additionally, the Azorhizobium genus was only detected in the ER phase. Overall, our findings suggested that several rhizosphere microbial communities had significant differences among three natural restoration stages (ER, MR, and LR) and the rhizosphere bacterial communities mainly appeared in the early restoration stage can be preferred for remediation of pollution soil in Xikuangshan.

Rhizosphere Bacteria in Plant Growth Promotion, Biocontrol, and Bioremediation of Contaminated Sites: A Comprehensive Review of Effects and Mechanisms

Agriculture in the 21st century is facing multiple challenges, such as those related to soil fertility, climatic fluctuations, environmental degradation, urbanization, and the increase in food demand for the increasing world population. In the meanwhile, the scientific community is facing key challenges in increasing crop production from the existing land base. In this regard, traditional farming has witnessed enhanced per acre crop yields due to irregular and injudicious use of agrochemicals, including pesticides and synthetic fertilizers, but at a substantial environmental cost. Another major concern in modern agriculture is that crop pests are developing pesticide resistance. Therefore, the future of sustainable crop production requires the use of alternative strategies that can enhance crop yields in an environmentally sound manner. The application of rhizobacteria, specifically, plant growth-promoting rhizobacteria (PGPR), as an alternative to chemical pesticides has gained much attention from the scientific community. These rhizobacteria harbor a number of mechanisms through which they promote plant growth, control plant pests, and induce resistance to various abiotic stresses. This review presents a comprehensive overview of the mechanisms of rhizobacteria involved in plant growth promotion, biocontrol of pests, and bioremediation of contaminated soils. It also focuses on the effects of PGPR inoculation on plant growth survival under environmental stress. Furthermore, the pros and cons of rhizobacterial application along with future directions for the sustainable use of rhizobacteria in agriculture are discussed in depth.

Cadmium Bioremediation Potential of Bacillus sp. and Cupriavidus sp

Heavy metals are extremely toxic and their presence in the environment is a known risk factor. Out of them, cadmium is known for its fatal effects on the environment, humans and soil. Bioremediation offers an economical solution for detoxifying such metals. So, the present study aimed to isolate Bacillus sp. and Cupriavidus sp. from the cadmium contaminated soils and studied their cadmium bioremediation potential. Strains that have exhibited good tolerance upto 1000 ppm and 1500 ppm of cadmium concentration and good absorption to cadmium were studied by scanning electron microscopy. An increase in the size of the bacterial cells was observed. The absorption of cadmium by bacterial cells was further confirmed by atomic absorption spectroscopy and found that the sorption rate of Bacillus sp. ECd004 was 87% and of Cupriavidus sp. SCd005 was 90%. Furthermore, these strains were exposed to cadmium contaminated soil in the form of bioformulations and their role in the rate of seed germination of Vigna radiata and Cicer aertinum and impact on seedlings growth was determined. Seed germination and growth rate was found to be double in comparison to the negative control. This investigation proves their efficacy to use in highly cadmium contaminated soils making them a suitable choice for bioremediation.

Characterization of plant growth-promoting rhizobacterial isolates associated with food plants in South Africa

The region around the plant root referred to as the rhizosphere, is the zone where various microbial activity occurs. It performs crucial functions such as increasing the uptake of nutrients for plant development and preventing plant against plant pathogens. Keeping in mind the beneficial role performed by rhizospheric microorganisms, rhizobacterial species were isolated from the maize and soybean plant's rhizosphere. The isolated microorganisms were evaluated for their biochemical characteristics, plant growth-promoting potentials, tolerance to different environmental conditions, and their antifungal activity against Fusarium graminearum, a fungal pathogen that infects maize. The rhizobacterial isolates with multiple plant growth-promoting potentials were identified as Bacillus spp (80.77%), Rhodocyclaceae bacterium (3.85%), Enterococcus spp (3.85%). Massilia spp (3.85%. and Pseudomonas (7.69%) species based on their 16S rRNA molecular characterization. The bacterial isolates possessed antifungal activities against Fusarium graminearum, promote maize and soybeans seed under laboratory conditions, and exhibited different levels of tolerance to pH, temperature, salt, and heavy metal. Based on this, the whole genome sequencing of Bacillus sp. OA1, Pseudomonas rhizosphaerea OA2, and Pseudomonas sp. OA3 was performed using Miseq Illumina system to determine the functional genes and secondary metabolites responsible for their plant growth-promoting potential Thus, the result of this research revealed that the selected bacterial isolates possess plant growth-promoting potentials that can make them a potential candidate to be employed as microbial inoculants for protecting plants against phytopathogens, environmental stress and increasing plant growth and productivity.

Isolation and Identification of Uranium Tolerant Phosphate-Solubilizing Bacillus spp. and Their Synergistic Strategies to U(VI) Immobilization

The remediation of uranium (U) through phosphate-solubilizing bacteria (PSB) is an emerging technique as well as an interesting phenomenon for transforming mobile U into stable minerals in the environment. While studies are well needed for in-depth understanding of the mechanism of U(VI) immobilization by PSB. In this study, two PSB were isolated from a U-tailing repository site. These bacterial strains (ZJ-1 and ZJ-3) were identified as Bacillus spp. by the sequence analysis of 16S ribosomal RNA (rRNA) genes. Incubation of PSB in liquid medium showed that the isolate ZJ-3 could solubilize more than 230 mg L^-1 P from glycerol-3-phosphate and simultaneously removed over 70% of 50 mg L^-1 U(VI) within 1 h. During this process, the rapid appearance of yellow precipitates was observed. The microscopic and spectroscopic analysis demonstrated that the precipitates were associated with U-phosphate compound in the form of saleeite-like substances. Besides, scanning electron microscopy coupled with energy-dispersive X-ray (SEM-EDS) and Fourier transform infrared spectroscopy (FTIR) analysis of the precipitates confirmed that the extracellular polymeric substances (EPS) might also play a key role in U sequestration. Furthermore, SEM and FTIR analysis revealed that part of U(VI) was adsorbed on the bacterial surface through cellular phosphate, hydroxy, carboxyl, and amide groups. This study provides new insights into the synergistic strategies enhancing U immobilization rates by Bacillus spp. that uses glycerol-3-phosphate as the phosphorus source, the process of which contributes to harmful pollutant biodegradation.

Endophyte Pseudomonas putida enhanced Trifolium repens L. growth and heavy metal uptake: A promising in-situ non-soil cover phytoremediation method of nonferrous metallic tailing

Non-soil cover phytoremediation is the most promising method for high heavy metal contaminated, pH imbalanced and oligotrophic tailing remediation. In this study, a promising method of tailing non-soil cover phytoremediation by endophyte assisting Trifolium repens L. was established. Endophytic Pseudomonas putida strain RE02, with great heavy metal detoxification ability, could colonize in both rhizosphere and endosphere of roots. With RE02 inoculation, the germination percentage of Trifolium repens L. seeds was improved form 40.33%, 45.33% and 56.67%-60.00%, 57.00% and 73.33% in 20 mg/kg Cd, 20 mg/kg Cr and 100 mg/kg Pb contained tailing. The LC50 (concentrations causing 50% mortality of seedlings) and IC50 (concentrations inhibiting the dry biomass by 50%) of Cd, Cr and Pb increased by 6.62, 4.87, 6.27, 4.28, 22.18 and 22.63 mg/kg respectively. Moreover, RE02 inoculation improved soil fertility that the available P and available K was dramatically enhanced in endophyte inoculated groups. Thus, plant NPK concentration was significantly enhanced by 16.72%, 30.55% and 3.81% respectively, and the total heavy metal uptake by 30.03-574.58%. Taken together, Trifolium repens L. successfully grew and developed in heavy metal contaminated, oligotrophic and pH imbalanced tailing, realizing non-soil cover phytoremediation by RE02 inoculation. Overall, this study provided a feasible and promising method for in-situ non-soil cover phytoremediation of tailing, laying a foundation for ecological restoration of tailing.

Elsayed E, El Enshasy HA. Role of Bacillus cereus in Improving the Growth and Phytoextractability of Brassica nigra (L.) K. Koch in Chromium Contaminated Soil

Plant growth-promoting rhizobacteria (PGPR) mediate heavy metal tolerance and improve phytoextraction potential in plants. The present research was conducted to find the potential of bacterial strains in improving the growth and phytoextraction abilities of Brassica nigra (L.) K. Koch. in chromium contaminated soil. In this study, a total of 15 bacterial strains were isolated from heavy metal polluted soil and were screened for their heavy metal tolerance and plant growth promotion potential. The most efficient strain was identified by 16S rRNA gene sequencing and was identified as Bacillus cereus. The isolate also showed the potential to solubilize phosphate and synthesize siderophore, phytohormones (indole acetic acid, cytokinin, and abscisic acid), and osmolyte (proline and sugar) in chromium (Cr+3) supplemented medium. The results of the present study showed that chromium stress has negative effects on seed germination and plant growth in B. nigra while inoculation of B. cereus improved plant growth and reduced chromium toxicity. The increase in seed germination percentage, shoot length, and root length was 28.07%, 35.86%, 19.11% while the fresh and dry biomass of the plant increased by 48.00% and 62.16%, respectively, as compared to the uninoculated/control plants. The photosynthetic pigments were also improved by bacterial inoculation as compared to untreated stress-exposed plants, i.e., increase in chlorophyll a, chlorophyll b, chlorophyll a + b, and carotenoid was d 25.94%, 10.65%, 20.35%, and 44.30%, respectively. Bacterial inoculation also resulted in osmotic adjustment (proline 8.76% and sugar 28.71%) and maintained the membrane stability (51.39%) which was also indicated by reduced malondialdehyde content (59.53% decrease). The antioxidant enzyme activities were also improved to 35.90% (superoxide dismutase), 59.61% (peroxide), and 33.33% (catalase) in inoculated stress-exposed plants as compared to the control plants. B. cereus inoculation also improved the uptake, bioaccumulation, and translocation of Cr in the plant. Data showed that B. cereus also increased Cr content in the root (2.71-fold) and shoot (4.01-fold), its bioaccumulation (2.71-fold in root and 4.03-fold in the shoot) and translocation (40%) was also high in B. nigra. The data revealed that B. cereus is a multifarious PGPR that efficiently tolerates heavy metal ions (Cr+3) and it can be used to enhance the growth and phytoextraction potential of B. nigra in heavy metal contaminated soil.

Metagenomic analysis for profiling of microbial communities and tolerance in metal-polluted pulp and paper industry wastewater

This work aimed to study the profiling and efficiency of microbial communities and their abundance in the pulp and paper industry wastewater, which contained toxic metals, high biological oxygen demands, chemical oxygen demand, and ions contents. Sequence alignment of the 16S rRNA V3-V4 variable region zone with the Illumina MiSeq framework revealed 25356 operating taxonomical units (OTUs) derived from the wastewater sample. The major phyla identified in wastewater were Proteobacteria, Bacteroidetes, Firmicutes, Chloroflexi, Actinobacteria, Spirochetes, Patesibacteria, Acidobacteria, and others including unknown microbes. The study showed the function of microbial communities essential for the oxidation and detoxifying of complex contaminants and design of effective remediation techniques for the re-use of polluted wastewater. Findings demonstrated that the ability of different classes of microbes to adapt and survive in metal-polluted wastewater irrespective of their relative distribution, as well as further attention can be provided to its use in the bioremediation process.

Successful Plant Growth-Promoting Microbes: Inoculation Methods and Abiotic Factors

Plant-microbe interactions have been the subject of several biotechnological studies, seeking sustainable development and environmental conservation. The inoculation of plant growth-promoting microbes (PGPM) in agricultural crops is considered an environmental-friendly alternative to chemical fertilization. Microbial inoculants are mainly inoculated onto seeds, roots and soil. PGPM improve plant growth by enhancing the availability of nutrients, the regulation of phytohormones, and by increasing plant tolerance against biotic and abiotic stresses. One of the main obstacles with PGPM research are the inconsistent results, which may be the result of inoculation methods and abiotic factors, such as soil (nutrient or heavy metal contents and pH), water availability, light intensity and temperature. This review addresses how the PGPM inoculants act on plant growth, what mechanisms they use to survive under stressful environmental conditions, and how inoculation methods and abiotic factors can interfere on the success of microbial inoculation in plants, serving as a basis for research on plants-microorganisms interaction.

Rhizosphere Microbiome Cooperations: Strategies for Sustainable Crop Production

Interactions between microorganisms and host plants determine the growth and development as well as the health of the host plant. Various microbial groups inhabit the rhizosphere, each with its peculiar function. The survival of each microbial group depends to a large extent on its ability to colonize the plant root and outcompete the native organisms. The role of the rhizospheric microbiome in enhancing plant growth has not been fully maximized. An understanding of the complexities of microbial interactions and factors affecting their assembly in the community is necessary to benefit maximally from the cooperations of various microbial communities for sustainable crop production. In this review, we outline the various organisms associated with the plant rhizosphere with emphasis on their interactions and mechanisms used in plant growth promotion.

Plant Growth Promoting Rhizobacteria (PGPR) as Green Bioinoculants: Recent Developments, Constraints, and Prospects

The quest for enhancing agricultural yields due to increased pressure on food production has inevitably led to the indiscriminate use of chemical fertilizers and other agrochemicals. Biofertilizers are emerging as a suitable alternative to counteract the adverse environmental impacts exerted by synthetic agrochemicals. Biofertilizers facilitate the overall growth and yield of crops in an eco-friendly manner. They contain living or dormant microbes, which are applied to the soil or used for treating crop seeds. One of the foremost candidates in this respect is rhizobacteria. Plant growth promoting rhizobacteria (PGPR) are an important cluster of beneficial, root-colonizing bacteria thriving in the plant rhizosphere and bulk soil. They exhibit synergistic and antagonistic interactions with the soil microbiota and engage in an array of activities of ecological significance. They promote plant growth by facilitating biotic and abiotic stress tolerance and support the nutrition of host plants. Due to their active growth endorsing activities, PGPRs are considered an eco-friendly alternative to hazardous chemical fertilizers. The use of PGPRs as biofertilizers is a biological approach toward the sustainable intensification of agriculture. However, their application for increasing agricultural yields has several pros and cons. Application of potential biofertilizers that perform well in the laboratory and greenhouse conditions often fails to deliver the expected effects on plant development in field settings. Here we review the different types of PGPR-based biofertilizers, discuss the challenges faced in the widespread adoption of biofertilizers, and deliberate the prospects of using biofertilizers to promote sustainable agriculture.

Effects of Contamination of Freshwater Habitat With Common Heavy Metals and Anions on the Prevalence of Human Adenoviruses and Enteroviruses

The occurrence and survival of enteric viruses in open surface waters can be impacted by a host of factors including fecal emission levels, seasonal variations, virus stability and the physicochemical parameters. In this research, we aimed to document the association between contaminations of water samples with human enteric viruses (adenoviruses and enteroviruses) from a freshwater lake with variations in chemical contaminants. We collected 216 water samples from October 2010 to April 2012, from a 4 km stretch along Lake Victoria (LV) basin in Homa Bay town located in the western region of Kenya. The samples were analyzed for the existence of human adenoviruses (HAdV) and human enteroviruses (HEV), using the nested PCR (nPCR). We also assessed in the water samples the levels of twelve chemical contaminants consisting of six heavy metal elements and six anions. About 8.3 % of the samples were found to be contaminated with the enteric viruses. The concentrations of the 12 chemical contaminants were found to be largely within the WHO suggested limits. Most of the chemical contaminants were not related to the detection rates of the viruses from the statistical analysis. However, some positive and negative associations between the viral genome's detection and the chemical concentrations were established for only three metals (Fe, Pb, Cd) and the PO4³⁻ Radical. Cd had a weak positive significant relationship with HAdV (rho = 0.146, p = 0.032) while Pb and Fe had a weak positive significant relationship with HEV genome detection (rho = 0.156, p = 0.022) and (rho = 0.148 and p = 0.029) respectively. There was a modest negative relationship between phosphate ions and HEV (rho = −0.174, p = 0.010). The results of our study do not provide support for the hypothesis of an association between the presence of human enteric viruses and the levels of twelve chemical contaminants.

Effects of physicochemical properties of Au cyanidation tailings on cyanide microbial degradation

The initial cyanide (CN^-) concentration and amount of co-contaminants in GCTs can inhibit bacterial growth and reduce the CN^--degrading ability of bacteria. Several microorganisms can biotransform a wide range of organic and inorganic industrial contaminants into nontoxic compounds. However, active enzymatic CN^- metabolism processes are mostly constrained by the physical and chemical characteristics of GCTs. High concentrations of toxic metal co-contaminants, such as, Pb, and Cr, and factors, such as pH, temperature, and oxygen concentration create oxidative stress and limit the CN^--degrading potential of cyanotrophic strains. The effects of such external and internal factors on the CN^--degrading ability of bacteria hinder the selection of suitable microorganisms for CN^- biodegradation. Therefore, understanding the effects of the physicochemical properties of GCTs on cyanobacteria strains can help identify suitable microbes and favorable environmental conditions to promote microbial growth and can also help design efficient CN^- biodegradation processes. In this review, we present a detailed analysis of the physicochemical properties of GCTs and their effects on microbial CN^- degradation.

Effects of rhizobia and arbuscular mycorrhizal fungi on yield, size distribution and fatty acid of soybean seeds grown under drought stress

Soybean (Glycine max L.) is among the most economically important legumes that provide more than 1/4 of food (for man) and animal feed. However, its yield is comparatively low, most especially under drought stress. The aim of this study therefore was to assess the ability of Rhizobium spp. and mycorrhizal fungi to enhance the yield, seed size and fatty acid content of soybean grown under semi-arid environment. Rhizobium sp. strain R1 was found to possess nitrogen-fixing gene coniferyl aldehyde dehydrogenase function while Rhizobium cellulosilyticum strain R3 was found to have nitrogen-fixing genes cysteine desulfurase SufS and cysteine desulfurase IscS activity. Soybean (Glycine max L) seeds inoculated with Rhizobium spp. and mycorrhizal fungi were cultivated in soil exposed to drought stress. Rhizobium spp. inoculation and mycorrhization alleviate drought stress and increase yield, size and fat content of soybean seeds. This increase in the aboveground parameters was accompanied with an increase in belowground mycorrhizal spore number, percentage root mycorrhization and aboveground shoot relative water content (RWC) in the dually inoculated (R1 + R3MY) soybean plants. In particular, the dually inoculated (R1 + R3MY) soybean plants revealed 34.3 g fresh weight, 15.1 g dry weight and soybean plants singly inoculated with Rhizobium sp. strain R1 (R1) produced more large seeds with 12.03 g dry weight. The non-inoculated (control) seeds contained a higher percentage of moisture content compared to the microbially amended seeds while seeds co-inoculated with Rhizobium cellulosilyticum strain R3 and mycorrhizal consortium revealed the highest percent (8.4 %) of fat. Several fatty acids that are of significant health benefits to humans were observed in the soybean seeds. In order to gain insights into the bacterial communities of rhizospheric soil collected at different stages of soybean growth, class-based Heat-map analysis was performed on the Miseq sequenced data. The core bacteria that were found in the rhizospheric soil were Verrumicrobia, Proteobacteria, Gemmatimonadetes, Firmicutes, Cyanobacteria, Chloroflexi, Bacteroidetes, Actinobacteria, Acidobacteria, Planctomycetes, Deinococcus thermus and Nitrospira suggesting that the rhizobia and fungi used in this study can also improve soil microbial diversity.

Endophytic inoculation coupled with soil amendment and foliar inhibitor ensure phytoremediation and argo-production in cadmium contaminated soil under oilseed rape-rice rotation system

Phytoremediation coupled with agro-production is a sustainable strategy for remediation of toxic metal contaminated farmlands without interrupting crop production. In this study, high accumulating oilseed rape was rotated with low accumulating rice to evaluate the effects of crop rotation on growth performance and uptake of cadmium (Cd) in plants. In this system, oilseed rape was inoculated with plant growth promoting endophyte (PGPE) consortium, and rice was applied with soil composite amendment and foliar inhibitor. The results showed, compared with rice monoculture, crop rotation coupled with superposition measure has potential to enhance yield, biomass and nutritional quality of both crops, as well as to increase Cd uptake in non-edible tissues of oilseed rape and to reduce Cd concentration in individual parts of rice, thus accelerating phytoextraction and ensuring food safety. These comprehensive management practices removed 7.03 and 7.91% total Cd from two experiment fields, respectively, in three years phytoremediation. These results demonstrated a feasible technical mode for phytoremediation coupled with argo-production in slightly Cd contaminated field, and also provided useful information for further investigation of interaction mechanisms between the rotated crops and biofortification measures.

Modification-bioremediation of copper, lead, and cadmium-contaminated soil by combined ryegrass (Lolium multiflorum Lam.) and Pseudomonas aeruginosa treatment

The principal objective of this study was to investigate the strengthened remediation effect and relevant mechanism of P. aeruginosa on ryegrass (Lolium multiflorum Lam.) for soil contaminated by Cu-Pb-Cd compound heavy metals. The results showed that the complex heavy metals' contamination had remarkable inhibiting effect on the growth of plants (P < 0.01), and the biomass of ryegrass's stem and leaves declined by 28.2%, while that of roots decreased by 34.7% after 45 days. The inoculation of P. aeruginosa promoted the growth of ryegrass in polluted soil, in which the biomass recovered to the same level of that in normal plant; the activity of both catalase and urease in the soil also increased strikingly (by 29.3% and 75.7%, respectively); the ratio of residual heavy metals in the soil decreased, while the acid extractable heavy metals increased notably. Therefore, the absorption and accumulation of ryegrass to the heavy metals in soil were improved to some extent; the bioconcentration factor of Cu, Pb, and Cd in ryegrass increased by 35.9%, 55.6%, and 283.5%, respectively. The exterior microorganism allowed the accumulation of Cu, Pb, and Cd in shoots of ryegrass increasing remarkably, while in roots, only the accumulation of Pb increased by 16.3%, and that of both Cu and Cd decreased. Besides, in the P. aeruginosa-inoculated system, the transfer factor of Cu and Cd in plants increased strikingly, while that of Pb decreased.

Improving hybrid Pennisetum growth and cadmium phytoremediation potential by using Bacillus megaterium BM18-2 spores as biofertilizer

Environmental pollution with heavy metals becomes an issue of serious concern worldwide. Cadmium is considered one which adversely affects living organisms. Recently, the usage of endophytic bacteria to enhance the plant growth and phytoremediation of heavy metals contaminated sites is gaining great attention. The current study focused on utilizing the spores of Bacillus megaterium BM18-2 as biofertilizer for enhancing the growth of Cd hyperaccumulator Hybrid Pennisetum and Cd tolerance of the plant. Therefore, the production of the highest proportion of BM18-2 spores in short incubation time was investigated using different culture media. The results revealed that the maximum proportion of BM18-2 spores (90%) was obtained following incubation for 48 h in Tryptone- yeast extract media (TY). Furthermore, several growth parameters of H. Pennisetum were shown to be significantly improved by inclusion of BM18-2 spores into Cd contaminated soil in contrast to non- inoculated plant. The chlorophyll concentration of the leaves rose by 5%, 13%, and 22.89% with increasing Cd concentration of soil (20, 40 and 60 mg/Kg, respectively). The percentage of total nitrogen content of the root, stem and leaf was increased due to the bacterial spores inoculation and the highest percentage was recorded in the leaf in all treatments. Moreover, Cd phytoremediation capacity of H. Pennisetum greatly enhanced with the application of BM18-2 spores into the soil. An obvious correlation was also observed between Cd accumulation and bacterial colonization where the Cd accumulation enhanced by 21.9%, 16.5%, and 94.6% and the maximum count of BM18-2 (27 × 10⁵, 194 × 10⁴,and 145 × 10⁴ CFU/g) were recorded in the root system in 20, 40, and 60 mg/Kg Cd spiked soil, respectively. Consequently, the spores of BM18-2 was proven to succeed as biofertilizer to improve growth of H. pennisetum during Cd stress which subsequently improved the phytoremediation of Cd contaminated soil.

Combined use of municipal solid waste biochar and bacterial biosorbent synergistically decreases Cd(II) and Pb(II) concentration in edible tissue of forage maize irrigated with heavy metal-spiked water

A pot experiment was carried out to evaluate the effect of a municipal solid waste (MSW) biochar and a bacterial strain on the forage maize growth and the concentration of lead (Pb) and cadmium (Cd) in the edible tissue of maize irrigated with water contaminated with Cd (5 mg L⁻¹) and Pb (100 mg L⁻¹). Experimental treatments included (i) bacterial strain at two levels: no bacterial strain and Enterobacter cloacae R7; (ii) MSW biochar at three levels: 0, 1, and 3% (w/w); and (iii) irrigation water quality at five levels: plants irrigated with 100% freshwater (FW), plants irrigated with 75%FW + 25% contaminated water (CW), plants irrigated with 50%FW + 50% CW, plants irrigated with 25%FW + 75% CW, and plants irrigated with 100% CW. The effect of various treatments on maize growth indices and concentration of Pb(II) and Cd(II) in the plant was significant at 5% level. The concentration of these metals in the shoot of plants irrigated with 75 and 100% CW was higher than the permissible limits for Cd(II) and Pb(II) in livestock feed. However, the concentration of these metals in the shoot of the plants irrigated with 25 and 50% CW was lower than the permissible limit for this use. In this study, the combined application of 3%biochar and E. cloacae R7 had a significant effect on increased root dry weight (ranging from 29 to 33%), shoot dry weight (ranging from 32 to 43%) and bacterial root colonization (ranging from 33 to 53%) and on reduced concentration of Pb (ranging from 78 to 80%) and Cd (ranging from 72 to 76%) of the shoot of maize plant (edible tissues used by livestock), which was below the permissible limits for livestock feed, compared to corresponding controls. According to the results of this study, to reduce the concentration of the heavy metals in forage maize shoot (below the permissible limits for livestock feed), it is suggested using heavy metal–contaminated water either in combination with freshwater (50 or 75% FW) or in combination with biochar and bacterial biosorbent, averting human/animal health risk.

Isolation and Characterization of Indigenous Plant Growth-Promoting Rhizobacteria (PGPR) from Cardamom Rhizosphere

The present study was conducted to explore the native plant growth-promoting (PGP) bacteria from cardamom rhizosphere in few districts of Kerala and Tamilnadu under cardamom cultivation. The isolates obtained were screened for their PGP characteristics and their beneficial effect on cardamom was evaluated. Of the total 88 isolates, ten were screened as promising based on their performance in growth promoting attributes such as production of indole acetic acid, gibberellic acid, siderophore, hydrogen cyanide, heavy metal tolerance and antibiotic resistance. Diazotrophy of the screened isolates were tested by nitrogenase assay and evaluated using the diversity of nif genes. Genetic analysis was carried out to assess the phylogenetic relationship using 16S rRNA sequencing. The phylogenetic analysis exhibited clear clustering of isolates into three phyla namely Firmicutes, Actinobacteria and γ-proteobacteria. Majority of the isolates were grouped into Bacillus and Pseudomonas at genus level. Three different plant inoculation study at nursery and field level, viz., Bacillus subtilis TAUC1, Bacillus subtilis TAUC2 and Pseudomonas putida TAUC10. The combined inoculation of bioinoculants were superior over individual inoculation with respect to growth, soil and plant nutrient content, biochemical constituents, rhizosphere population, soil enzyme activities and yield. Hence the present study reveals the potential effect of PGPR for bioinoculant production for enhancing growth and development of cardamom under field conditions.

Prospect of phytoremediation combined with other approaches for remediation of heavy metal-polluted soils

Accumulation of heavy metals in agricultural soils due to human production activities-mining, fossil fuel combustion, and application of chemical fertilizers/pesticides-results in severe environmental pollution. As the transmission of heavy metals through the food chain and their accumulation pose a serious risk to human health and safety, there has been increasing attention in the investigation of heavy metal pollution and search for effective soil remediation technologies. Here, we summarized and discussed the basic principles, strengths and weaknesses, and limitations of common standalone approaches such as those based on physics, chemistry, and biology, emphasizing their incompatibility with large-scale applications. Moreover, we explained the effects, advantages, and disadvantages of the combinations of common single repair approaches. We highlighted the latest research advances and prospects in phytoremediation-chemical, phytoremediation-microbe, and phytoremediation-genetic engineering combined with remediation approaches by changing metal availability, improving plant tolerance, promoting plant growth, improving phytoextraction and phytostabilization, etc. We then explained the improved safety and applicability of phytoremediation combined with other repair approaches compared to common standalone approaches. Finally, we established a prospective research direction of phytoremediation combined with multi-technology repair strategy.

Improvement of rice plant productivity by native Cr(VI) reducing and plant growth promoting soil bacteria Enterobacter cloacae

Rapid industrialization and anthropogenic activities have produced huge amount of noxious Cr(VI), which accumulate in the soil for longer period. As a consequence, that decreases rice plant productivity in contiguous agricultural field of Sukinda mining area, Odisha. Thus, the high Cr(VI) resistant native bacterial strain CTWI-06 was selected for the study, which depicted resistance to 3500 ppm of Cr(VI) and wide array of other metals. Under optimized condition, the multi-metal resistant bacteria reduced 94% Cr(VI) within 92 h and Cr(VI) reduction was confirmed by FTIR and XRD analysis. Plant growth promoting traits like N₂ fixation; phosphate (146.87 ppm), potassium (12.55 ppm) and Zn solubilization; ammonification; IAA production (114 μg mL^-1) and suppression of fungal phytopathogens such as Rhizoctonia solani (ITCC 2060) and Phytium debaryanum (ITCC 5488) were also recorded. The bacterial strain was identified as Enterobacter cloacae CTWI-06 by 16S rDNA sequence (Accession No. MG757378). It significantly improved growth traits as well as productivity of Mahalakshmi rice variety in pot culture. Thus, the potential Cr(VI) reducing and PGPB strain may be utilized for long term bioremediation of Cr(VI) in chromium contaminated soil and to maintain soil fertility.