Comparative transcriptome profiling reveals the reprogramming of gene networks under arsenic stress in Indian mustard

Phytobial remediation advances and application of omics and artificial intelligence: a review

Industrialization and urbanization increased the use of chemicals in agriculture, vehicular emissions, etc., and spoiled all environmental sectors. It causes various problems among living beings at multiple levels and concentrations. Phytoremediation and microbial association are emerging as a potential method for removing heavy metals and other contaminants from soil. The treatment uses plant physiology and metabolism to remove or clean up various soil contaminants efficiently. In recent years, omics and artificial intelligence have been seen as powerful techniques for phytobial remediation. Recently, AI and modeling are used to analyze large data generated by omics technologies. Machine learning algorithms can be used to develop predictive models that can help guide the selection of the most appropriate plant and plant growth-promoting rhizobacteria combination that is most effective at remediation. In this review, emphasis is given to the phytoremediation techniques being explored worldwide in soil contamination.

Transcriptomic analysis revealing the molecular response to arsenic stress in desert Eremostachys moluccelloides Bunge

The saline, alkaline environment of arid soils is conducive to the diffusion of the metalloid arsenic (As). Desert plants in this area are of great ecological importance and practical value. However, there are few studies on the mechanism of arsenic action in desert plants. Therefore, in this study, Eremostachys moluccelloides Bunge was treated with different concentrations of As2O5 [As(V)] to analyze the physiological, biochemical, and transcriptomic changes of its roots and leaves and to explore the molecular mechanism of its response to As(Ⅴ) stress. The activities of catalase, superoxidase, peroxidase, and the contents of malondialdehyde and proline in roots and leaves first increased and then decreased under the As(Ⅴ) stress of different concentrations. The content of As was higher in roots than in leaves, and the As content was positively correlated with As(Ⅴ) stress concentration. In the differentially expressed gene analysis, the key enzymes of the oxidative stress response in roots and leaves were significantly enriched in the GO classification. In the KEGG pathway, genes related to the abscisic acid signal transduction pathway were co-enriched and up-regulated in roots and leaves. The related genes in the phenylpropanoid biosynthesis pathway were significantly enriched and down-regulated only in roots. In addition, the transcription factors NAC, HB-HD-ZIP, and NF-Y were up-regulated in roots and leaves. These results suggest that the higher the As(V) stress concentration, the more As is taken up by roots and leaves of E. molucelloides Bunge. In addition to causing greater oxidative damage, this may interfere with the production of secondary metabolites. Moreover, it may improve As(V) tolerance by regulating abscisic acid and transcription factors. The results will deepen our understanding of the molecular mechanism of As(Ⅴ) response in E. moluccelloides Bunge, lay the foundation for developing and applying desert plants, and provide new ideas for the phytoremediation of As pollution in arid areas.

Comprehensive mechanisms of heavy metal toxicity in plants, detoxification, and remediation

Natural and anthropogenic causes are continually growing sources of metals in the ecosystem; hence, heavy metal (HM) accumulation has become a primary environmental concern. HM contamination poses a serious threat to plants. A major focus of global research has been to develop cost-effective and proficient phytoremediation technologies to rehabilitate HM-contaminated soil. In this regard, there is a need for insights into the mechanisms associated with the accumulation and tolerance of HMs in plants. It has been recently suggested that plant root architecture has a critical role in the processes that determine sensitivity or tolerance to HMs stress. Several plant species, including those from aquatic habitats, are considered good hyperaccumulators for HM cleanup. Several transporters, such as the ABC transporter family, NRAMP, HMA, and metal tolerance proteins, are involved in the metal acquisition mechanisms. Omics tools have shown that HM stress regulates several genes, stress metabolites or small molecules, microRNAs, and phytohormones to promote tolerance to HM stress and for efficient regulation of metabolic pathways for survival. This review presents a mechanistic view of HM uptake, translocation, and detoxification. Sustainable plant-based solutions may provide essential and economical means of mitigating HM toxicity.

Genome-wide analysis of Catalase gene family reveal insights into abiotic stress response mechanism in Brassica juncea and B. rapa

Environmental stresses affect the yield and productivity of Brassica crops. Catalases are important antioxidant enzymes involved in reducing excess hydrogen peroxide produced by environmental stresses. In the present study, nine and seven CAT family members in two oilseed Brassica species (B. juncea and B. rapa) were identified with complete characterization based on gene and protein structure. Phylogenetic classification categorized CAT proteins into three classes and differentiated the monocot and dicot-specific CAT proteins. Further, the gene and protein characterizations revealed a high degree of conservation across the CAT family members. Differences were observed in the CAT-HEME binding affinity in CAT1, CAT2, and CAT3 isozymes, which could suggest their differential enzyme activities in different conditions. Furthermore, protein-protein interaction with other antioxidant proteins suggested their coordinated role in ROS scavenging mechanisms. Notably, the differential gene expression of BjuCATs and BraCATs and CAT enzyme activities suggested their crucial roles in major abiotic stresses faced by Brassica species. Promoter analysis in BjuCATs and BraCATs suggested the presence of abiotic-stress responsive cis-regulatory elements. Gene regulatory network analysis suggested miRNA and TF mediated stress response in BjuCATs and BraCATs. CAT family screening and characterization in Brassica sp. has established a basic ground for further functional validation in abiotic and heavy-metal stresses which can help in developing stress tolerant crops.

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.

Molecular insight into arsenic uptake, transport, phytotoxicity, and defense responses in plants: a critical review

A critical investigation into arsenic uptake and transportation, its phytotoxic effects, and defense strategies including complex signaling cascades and regulatory networks in plants. The metalloid arsenic (As) is a leading pollutant of soil and water. It easily finds its way into the food chain through plants, more precisely crops, a common diet source for humans resulting in serious health risks. Prolonged As exposure causes detrimental effects in plants and is diaphanously observed through numerous physiological, biochemical, and molecular attributes. Different inorganic and organic As species enter into the plant system via a variety of transporters e.g., phosphate transporters, aquaporins, etc. Therefore, plants tend to accumulate elevated levels of As which leads to severe phytotoxic damages including anomalies in biomolecules like protein, lipid, and DNA. To combat this, plants employ quite a few mitigation strategies such as efficient As efflux from the cell, iron plaque formation, regulation of As transporters, and intracellular chelation with an array of thiol-rich molecules such as phytochelatin, glutathione, and metallothionein followed by vacuolar compartmentalization of As through various vacuolar transporters. Moreover, the antioxidant machinery is also implicated to nullify the perilous outcomes of the metalloid. The stress ascribed by the metalloid also marks the commencement of multiple signaling cascades. This whole complicated system is indeed controlled by several transcription factors and microRNAs. This review aims to understand, in general, the plant-soil-arsenic interaction, effects of As in plants, As uptake mechanisms and its dynamics, and multifarious As detoxification mechanisms in plants. A major portion of this article is also devoted to understanding and deciphering the nexus between As stress-responsive mechanisms and its underlying complex interconnected regulatory networks.

Water and soil contaminated by arsenic: the use of microorganisms and plants in bioremediation

Owing to their roles in the arsenic (As) biogeochemical cycle, microorganisms and plants offer significant potential for developing innovative biotechnological applications able to remediate As pollutions. This possible use in bioremediation processes and phytomanagement is based on their ability to catalyse various biotransformation reactions leading to, e.g. the precipitation, dissolution, and sequestration of As, stabilisation in the root zone and shoot As removal. On the one hand, genomic studies of microorganisms and their communities are useful in understanding their metabolic activities and their interaction with As. On the other hand, our knowledge of molecular mechanisms and fate of As in plants has been improved by laboratory and field experiments. Such studies pave new avenues for developing environmentally friendly bioprocessing options targeting As, which worldwide represents a major risk to many ecosystems and human health.

Arsenic acquisition, toxicity and tolerance in plants - From physiology to remediation: A review

Globally, environmental contamination by potentially noxious metalloids like arsenic is becoming a critical concern to the living organisms. Arsenic is a non-essential metalloid for plants and can be acclimatised in plants to toxic levels. Arsenic acquisition by plants poses serious health risks in human due to its entry in the food chain. High arsenic regimes disturb plant water relations, promote the generation of reactive oxygen species (ROS) and induce oxidative outburst in plants. This review evidences a conceivable tie-up among arsenic levels, speciation, its availability, uptake, acquisition, transport, phytotoxicity and arsenic detoxification in plants. The role of different antioxidant enzymes to confer plant tolerance towards the enhanced arsenic distress has also been summed up. Additionally, the mechanisms involved in the modulation of different genes coupled with arsenic tolerance have been thoroughly discussed. This review is intended to present an overview to rationalise the contemporary progressions on the recent advances in phytoremediation approaches to overcome ecosystem contamination by arsenic.

Regulatory hubs and strategies for improving heavy metal tolerance in plants: Chemical messengers, omics and genetic engineering

Heavy metal (HM) accumulation in the agricultural soil and its toxicity is a major threat for plant growth and development. HMs disrupt functional integrity of the plants, induces altered phenological and physiological responses and slashes down qualitative crop yield. Chemical messengers such as phytohormones, plant growth regulators and gasotransmitters play a crucial role in regulating plant growth and development under metal toxicity in plants. Understanding the intricate network of these chemical messengers as well as interactions of genes/metabolites/proteins associated with HM toxicity in plants is necessary for deciphering insights into the regulatory circuit involved in HM tolerance. The present review describes (a) the role of chemical messengers in HM-induced toxicity mitigation, (b) possible crosstalk between phytohormones and other signaling cascades involved in plants HM tolerance and (c) the recent advancements in biotechnological interventions including genetic engineering, genome editing and omics approaches to provide a step ahead in making of improved plant against HM toxicities.

Metabolic Profiles of Brassica juncea Roots in Response to Cadmium Stress

Brassica juncea has great application potential in phytoremediation of cadmium (Cd)-contaminated soil because of its excellent Cd accumulating and high biomass. In this study, we compared the effects of Cd under 48 h and 7 d stress in roots of Brassica juncea using metabolite profiling. The results showed that many metabolic pathways and metabolites in Brassica juncea roots were altered significantly in response to Cd stress. We found that significant differences in levels of amino acids, organic acids, carbohydrates, lipids, flavonoids, alkaloids, and indoles were induced by Cd stress at different times, which played a pivotal role in the adaptation of Brassica juncea roots to Cd stress. Meanwhile, Brassica juncea roots could resist 48 h Cd stress by regulating the biosynthesis of amino acids, linoleic acid metabolism, aminoacyl-tRNA biosynthesis, glycerophospholipid metabolism, ABC transporters, arginine biosynthesis, valine, leucine and isoleucine biosynthesis, and alpha-linolenic acid metabolism; however, they regulated alpha-linolenic acid metabolism, glycerophospholipid metabolism, ABC transporters, and linoleic acid metabolism to resist 7 d Cd stress. A metabolomic expedition to the response of Brassica juncea to Cd stress will help to comprehend its tolerance and accumulation mechanisms of Cd.