Fungal and metabolome diversity of the rhizosphere and endosphere of Phragmites australis in an AMD-polluted environment

Bioindicator responses to extreme conditions: Insights into pH and bioavailable metals under acidic metal environments

Acid mine drainage (AMD) caused environmental risks from heavy metal pollution, requiring treatment methods such as chemical precipitation and biological treatment. Monitoring and adapting treatment processes was crucial for success, but cost-effective pollution monitoring methods were lacking. Using bioindicators measured through 16S rRNA was a promising method to assess environmental pollution. This study evaluated the effects of AMD on ecological health using the ecological risk index (RI) and the Risk Assessment Code (RAC) indices. Additionally, we also examined how acidic metal stress affected the diversity of bacteria and fungi, as well as their networks. Bioindicators were identified using linear discriminant analysis effect size (LEfSe), Partial least squares regression (PLS-R), and Spearman analyses. The study found that Cd, Cu, Pb, and As pose potential ecological risks in that order. Fungal diversity decreased by 44.88% in AMD-affected areas, more than the 33.61% decrease in bacterial diversity. Microbial diversity was positively correlated with pH (r = 0.88, p = 0.04) and negatively correlated with bioavailable metal concentrations (r = -0.59, p = 0.05). Similarly, microbial diversity was negatively correlated with bioavailable metal concentrations (bio_Cu, bio_Pb, bio_Cd) (r = 0.79, p = 0.03). Acidiferrobacter and Thermoplasmataceae were prevalent in acidic metal environments, while Puia and Chitinophagaceae were identified as biomarker species in the control area (LDA>4). Acidiferrobacter and Thermoplasmataceae were found to be pH-tolerant bioindicators with high reliability (r = 1, P < 0.05, BW > 0.1) through PLS-R and Spearman analysis. Conversely, Puia and Chitinophagaceae were pH-sensitive bioindicators, while Teratosphaeriaceae was a potential bioindicator for Cu-Zn-Cd metal pollution. This study identified bioindicator species for acid and metal pollution in AMD habitats. This study outlined the focus of biological monitoring in AMD acidic stress environments, including extreme pH, heavy metal pollutants, and indicator species. It also provided essential information for heavy metal bioremediation, such as the role of omics and the effects of organic matter on metal bioavailability.

Unlocking water potential in drylands: Quicklime and fly ash enhance soil microbiome structure, ecological networks and function in acid mine drainage water-irrigated agriculture

In water-stressed regions, treated acid mine drainage (AMD) water for irrigated agriculture is a potential solution to address freshwater scarcity. However, a significant knowledge gap exists on the short and long-term effects of treated AMD water on soil health. This study used high-throughput Illumina sequencing and predictive metagenomic profiling to investigate the impact of untreated AMD (AMD), quicklime- (A1Q and A2Q) and quicklime and fly ash-treated AMD water (AFQ) irrigation on soil bacterial diversity, co-occurrence networks and function. Results showed that untreated AMD water significantly increased soil acidity, electrical conductivity (EC), sulfate (SO42-), and heavy metals (HM), including reduced microbial diversity, disrupted interaction networks, and functional capacity. pH, EC, Cu, and Pb were identified as key environmental factors shaping soil microbial diversity and structure. Predominantly, Pseudomonas, Ralstonia picketti, Methylotenera KB913035, Brevundimonas vesicularis, and Methylobacteriumoryzae, known for their adaptability to acidic conditions and metal resistance, were abundant in AMD soils. However, soils irrigated with treated AMD water exhibited significantly reduced acidity (pH > 6.5), HM and SO42- levels, with an enrichment of a balanced bacterial taxa associated with diverse functions related to soil health and agricultural productivity. These taxa included Sphingomonas, Pseudoxanthomonas, Achromobacter, Microbacterium, Rhodobacter, Clostridium, Massillia, Rhizobium, Paenibacillus, and Hyphomicrobium. Moreover, treated AMD water contributed to higher connectivity and balance within soil bacterial co-occurrence networks compared to untreated AMD water. These results show that quicklime/fly ash treatments can help lessen impacts of AMD water on soil microbiome and health, suggesting its potential for irrigated agriculture in water-scarce regions.

Metabolomic Evenness Underlies Intraspecific Differences Among Lineages of a Wetland Grass

The metabolome represents an important functional trait likely important to plant invasion success, but we have a limited understanding of whether the entire metabolome or targeted groups of compounds confer an advantage to invasive as compared to native taxa. We conducted a lipidomic and metabolomic analysis of the cosmopolitan wetland grass Phragmites australis. We classified features into metabolic pathways, subclasses, and classes. Subsequently, we used Random Forests to identify informative features to differentiate five phylogeographic and ecologically distinct lineages: European native, North American invasive, North American native, Gulf, and Delta. We found that lineages had unique phytochemical fingerprints, although there was overlap between the North American invasive and North American native lineages. Furthermore, we found that divergence in phytochemical diversity was driven by compound evenness rather than metabolite richness. Interestingly, the North American invasive lineage had greater chemical evenness than the Delta and Gulf lineages but lower evenness than the North American native lineage. Our results suggest that metabolomic evenness may represent a critical functional trait within a plant species. Its role in invasion success, resistance to herbivory, and large-scale die-off events common to this and other plant species remain to be investigated.

The effects of long-term hexabromocyclododecanes contamination on microbial communities in the microcosms

The adaptation of microbial community to the long-term contamination of hexabromocyclododecanes (HBCDs) has not been well studied. Our previous study found that the HBCDs contamination in the microcosms constructed of sediments from two different mangrove forests in 8 months resulted in serious acidification (pH2-3). This study reanalyzed previous sequencing data and compared them with data after 20 months to investigate the adaptive properties of microbial communities in the stress of HBCDs and acidification. It hypothesized that the reassembly was based on the fitness of taxa. The results indicated that eukaryotes and fungi might have better adaptive capacity to these deteriorated habitats. Eukaryotic taxa Eufallia and Syncystis, and fungal taxa Wickerhamomyces were only detected after 20 months of contamination. Moreover, eukaryotic taxa Caloneis and Nitzschia, and fungal taxa Talaromyces were dominant in most of microbial communities (14.467-95.941%). The functional compositions were sediment-dependent and more divergent than community reassemblies. Network and co-occurrence analysis suggested that acidophiles such as Acidisoma and Acidiphilium were gaining more positive relations in the long-term stress. The acidophilic taxa and genes involved in resistance to the acidification and toxicity of HBCDs were enriched, for example, bacteria Acidisoma and Acidiphilium, archaea Thermogymnomonas, and eukaryotes Nitzschia, and genes kdpC, odc1, polA, gst, and sod-2. These genes involved in oxidative stress response, energy metabolism, DNA damage repair, potassium transportation, and decarboxylation. It suggested that the microbial communities might cope with the stress from HBCDs and acidification via multiple pathways. The present research shed light on the evolution of microbial communities under the long-term stress of HBCDs contamination and acidification.

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

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

Trends in Harnessing Plant Endophytic Microbiome for Heavy Metal Mitigation in Plants: A Perspective

Plant microbiomes represent dynamic entities, influenced by the environmental stimuli and stresses in the surrounding conditions. Studies have suggested the benefits of commensal microbes in improving the overall fitness of plants, besides beneficial effects on plant adaptability and survival in challenging environmental conditions. The concept of 'Defense biome' has been proposed to include the plant-associated microbes that increase in response to plant stress and which need to be further explored for their role in plant fitness. Plant-associated endophytes are the emerging candidates, playing a pivotal role in plant growth, adaptability to challenging environmental conditions, and productivity, as well as showing tolerance to biotic and abiotic stresses. In this article, efforts have been made to discuss and understand the implications of stress-induced changes in plant endophytic microbiome, providing key insights into the effects of heavy metals on plant endophytic dynamics and how these beneficial microbes provide a prospective solution in the tolerance and mitigation of heavy metal in contaminated sites.

Regulation mechanism of plant response to heavy metal stress mediated by endophytic fungi

Endophytic fungi exist widely in plants and play an important role in the growth and adaptation of plants. They could be used in phytoremediation techniques against heavy metal contaminated soil since beneficial microbial symbionts can endow plants with resistance to external heavy metal stresses. This review summarized the regulation mechanism of plant response to heavy metal stress mediated by endophytic fungi. Potential endophytic fungi in enhancing plant's adaption to heavy metal stresses include arbuscular mycorrhizal fungi, dark septate endophytic fungi, plant growth promoting endophytic fungi. The mechanisms involve coevolution strategy, immune regulation and detoxification transport to improve the ability of plants to adapt to heavy metal stress. They can increase the synthesis of host hormones and maintaining the balance of endogenous hormones, strengthen osmotic regulation, regulate carbon and nitrogen metabolism, and increase immune activity, antioxidant enzyme and glutathione activity. They also help to improve the detoxification transport and heavy metal emission capacity of the host by significantly producing iron carrier, metallothionein and 1-aminocyclopropane-1-carboxylic acid deaminase. The combination of endophytic fungi and hyperaccumulation plants provides a promising technology for the ecological restoration of heavy metal contaminated soil. Endophytic fungi reserves further development on enhancing host plant's adaptability to heavy metal stresses.

Role of plant growth-promoting rhizobacteria in boosting the phytoremediation of stressed soils: Opportunities, challenges, and prospects

Soil is considered as a vital natural resource equivalent to air and water which supports growth of the plants and provides habitats to microorganisms. Changes in soil properties, productivity, and, inevitably contamination/stress are the result of urbanisation, industrialization, and long-term use of synthetic fertiliser. Therefore, in the recent scenario, reclamation of contaminated/stressed soils has become a potential challenge. Several customized, such as, physical, chemical, and biological technologies have been deployed so far to restore contaminated land. Among them, microbial-assisted phytoremediation is considered as an economical and greener approach. In recent decades, soil microbes have successfully been used to improve plants' ability to tolerate biotic and abiotic stress and strengthen their phytoremediation capacity. Therefore, in this context, the current review work critically explored the microbial assisted phytoremediation mechanisms to restore different types of stressed soil. The role of plant growth-promoting rhizobacteria (PGPR) and their potential mechanisms that foster plants' growth and also enhance phytoremediation capacity are focussed. Finally, this review has emphasized on the application of advanced tools and techniques to effectively characterize potent soil microbial communities and their significance in boosting the phytoremediation process of stressed soils along with prospects for future research.

Experimental Research on the Remediation Ability of Four Wetland Plants on Acid Mine Drainage

In order to study the economical, efficient, and environmentally friendly techniques for the treatment of acid mine drainage (AMD), this paper investigated the effects of watering with AMD on the growth condition, the resilience of four wetland plants, as well as the uptake and transport of pollutants by plants. The results showed that Typha orientalis was more resistant to AMD (irrigation with AMD increased its catalase activity and glutathione content and promoted its growth), so it was suitable for treating high concentrations of AMD (SO42− ≈ 9400 mg/L); Cyperus glomeratus was suitable for treating medium concentrations of AMD (SO42− ≈ 4600 mg/L); and Scirpus validus and Phragmites australis could be used to treat low concentrations of AMD (SO42− ≈ 2300 mg/L). All four plants could be used for phytoextraction for Mn-contaminated water (TF > 1). Phragmites australis could be used for phytoextraction for Zn-contaminated water, and the other three plants could be used for phytostabilisation for Zn-contaminated water (TF < 1); the microbial biomass in the soil was affected not only by the concentration of AMD but also by plant species. This study provides a scientific basis for the phytoremediation technology of AMD.

A critical review of phytoremediation for acid mine drainage-impacted environments

Acid mine drainage (AMD), a waste product of mining activities containing sulfates, iron and heavy metals, causes severe environmental degradation and pose risks to human health and sustainable development. Areas impacted by AMD are lacking remediation techniques that holistically address the ecologic, social, and economic needs of affected communities, for which phytoremediation is a promising solution. This review article introduces AMD and AMD-impacted environments and critically discusses phytomanagement, phytoprotection, and phytorestoration approaches towards AMD-impacted environments. Continued research and application of such approaches will help optimize resource and revenue-generating potentials, address biodiversity loss and carbon storage concerns of climate change, and promote sustainable agricultural management. With a focus on energy crops, phytomining critical elements, carbon storage, co-cropping, allelopathy, and ecosystem restoration, this review examines phytoremediation research that addresses positive economic and environmental opportunities for AMD-impacted environments.

Heavy Metal Stress Alleviation Through Omics Analysis of Soil and Plant Microbiome

Heavy metal (HM) contamination of soil and water resources is a global concern, which not only limits crop yield and quality, but also has serious environmental effects. Due to the non-biodegradable nature and toxicity, high concentration of HMs in food and environment is a serious threat to the entire ecosystem. Moreover, the target of supplying safe and quality food to the rising human population (expected to reach ~9–10 bn by the year 2050), necessitates effective treatment of the HM-contaminated soil. Various microbe-mediated bioremediation strategies such as biosorption, bioprecipiation, biostimulation, etc., have been found to be effective in uptake and conversion of HMs to less toxic forms. Further, in the past few years, the use of soil and plant-associated microbiome for HM stress alleviation is gaining attention among the scientific community. In general, microbes are spectacular in being dynamic and more responsive to environmental conditions in comparison to their host plants. Moreover, with the advancements in high throughput sequencing technologies, the focus is eventually shifting from just structural characterization to functional insights into the microbiome. The microbes inhabiting the HM-contaminated environments or associated with HM-tolerant plants are a source for exploring HM-tolerant microbial communities, which could be used for enhancing bioremediation efficiency and conferring HM tolerance in plants. This review discusses the application of omics techniques including metagenomics, metatranscriptomics, metaproteomics, and metabolomics, for rapid and robust identification of HM-tolerant microbial communities, mining novel HM resistance genes, and fabricating the HM resistome.

Correlations Between Root Metabolomics and Bacterial Community Structures in the Phragmites australis Under Acid Mine Drainage-Polluted Wetland Ecosystem

Despite root microecology playing critical role in plant growth and fidelity, relatively few studies have focused on the link between the microbial communities and root metabolome in the aquatic macrophytes under heavy metal (HM) pollution. Using high-throughput metagenomic sequencing, targeted metabolomics and community-level physiological profile analyses, we investigated the symbiotic associations between Phragmites australis with rhizospheric bacterial communities under differing acid mine drainage (AMD) pollution. Results indicated that AMD pollution and root localization significantly affected root metabolome profiles. Higher accumulation of adenosine monophosphate, inosine, methionine, carnitine and dimethylglycine were observed in the rhizosphere under AMD than non-AMD habitat. Overall, the bacterial diversity and richness, and functional (metabolic) diversity were lower under high-AMD pollution. While non-AMD site was enriched with members of phylum Firmicutes, Proteobacteria were the most abundant taxa in the rhizosphere and endosphere under AMD-polluted sites. Further, plant growth promoting rhizobacteria (Rhizobium, Delftia, Bradyrhizobium, and Mesorhizobium) and metal-tolerant bacteria (Bacillus, Arthrobacter, Massilia and Methylocystis) were most abundant in AMD-polluted than non-AMD habitat. Finally, pH, TDS (total dissolved solids), Cu, Cr, Fe, and Zn content were the key environmental factors that strongly contributed to the spatial perturbation of rhizospheric metabolites, proteobacterial and acidobacterial taxa. Overall, the study linked the differential endospheric and rhizospheric bacterial community and metabolite profiles in P. australis under AMD environment and provided insights into HM adaptability and phytoremediation potential.

Effects of Oat Varieties and Growing Locations on Seed-Borne Fungal Communities

Many species of seed-borne fungi are closely allied with seed varieties and growing regions, including many seed-borne pathogens, but their species richness and distribution remain largely unknown. This study was conducted to explore the seed-borne fungal composition, abundance and diversity in Avena sativa (B7) and A. nuda (B2) seed samples collected from Baicheng (BB), Dingxi (DB) and Haibei (HB) city, using Illumina sequencing techniques. Our results show that a total of 543,707 sequences were obtained and these were assigned to 244 operational taxonomic units (OTUs) with 97% similarity. Oat varieties and growing locations had a significant difference on seed-borne fungal diversity. HB had a higher fungal diversity than BB and DB, Shannon diversity and ACE richness index of fungal in HB seeds was significantly higher than in BB and DB (P < 0.05). In different varieties, both taxon richness and evenness of B7 seeds was significantly higher than B2 (P < 0.05). A total of 4 fungal phyla and 26 fungal genera were detected. Ascomycota was the dominant phylum and Alternaria sp. was the most abundant genus in B2 and B7 oat seeds from different regions. Mycosphaerella sp. had a higher abundance in HB7 and DB7, respectively, Epicoccum sp. had a higher abundance in HB7 and BB7. The results of alpha and beta diversity analysis revealed the presence of different effects in fungal communities of different varieties and regions of oat, especially in seed pathogenic fungi distribution. Structural equation modeling also explained oat varieties and growing regions have significant influences on seed-borne fungal abundance, composition and diversity. This study demonstrated that the differences of varieties and regions are the main factors resulting in the changes of seed-borne fungal community of oat.

Microbial Community Diversity Dynamics in Acid Mine Drainage and Acid Mine Drainage-Polluted Soils: Implication on Mining Water Irrigation Agricultural Sustainability

Environmental degradation related to mining-generated acid mine drainage (AMD) is a major global concern, contaminating surface and groundwater sources, including agricultural land. In the last two decades, many developing countries are expanding agricultural productivity in mine-impacted soils to meet food demand for their rapidly growing population. Further, the practice of AMD water (treated or untreated) irrigated agriculture is on the increase, particularly in water-stressed nations around the world. For sustainable agricultural production systems, optimal microbial diversity, and functioning is critical for soil health and plant productivity. Thus, this review presents up-to-date knowledge on the microbial structure and functional dynamics of AMD habitats and AMD-impacted agricultural soils. The long-term effects of AMD water such as soil acidification, heavy metals (HM), iron and sulfate pollution, greatly reduces microbial biomass, richness, and diversity, impairing soil health plant growth and productivity, and impacts food safety negatively. Despite these drawbacks, AMD-impacted habitats are unique ecological niches for novel acidophilic, HM, and sulfate-adapted microbial phylotypes that might be beneficial to optimal plant growth and productivity and bioremediation of polluted agricultural soils. This review has also highlighted the impact active and passive treatment technologies on AMD microbial diversity, further extending the discussion on the interrelated microbial diversity, and beneficial functions such as metal bioremediation, acidity neutralization, symbiotic rhizomicrobiome assembly, and plant growth promotion, sulfates/iron reduction, and biogeochemical N and C recycling under AMD-impacted environment. The significance of sulfur-reducing bacteria (SRB), iron-oxidizing bacteria (FeOB), and plant growth promoting rhizobacteria (PGPRs) as key players in many passive and active systems dedicated to bioremediation and microbe-assisted phytoremediation is also elucidated and discussed. Finally, new perspectives on the need for future studies, integrating meta-omics and process engineering on AMD-impacted microbiomes, key to designing and optimizing of robust active and passive bioremediation of AMD-water before application to agricultural production is proposed.

Microbial Spectra, Physiological Response and Bioremediation Potential of Phragmites australis for Agricultural Production

Common reed (Phragmites australis) can invade and dominate in its natural habitat which is mainly wetlands. It can tolerate harsh environments as well as remediate polluted and environmental degraded sites such as mine dumps and other polluted wastelands. For this reason, this can be a very critical reed to reclaim wastelands for agricultural use to ensure sustainability. The present review manuscript examined the microbial spectra of P. australis as recorded in various recent studies, its physiological response when growing under stress as well as complementation between rhizosphere microbes and physiological responses which result in plant growth promotion in the process of phytoremediation. Microbes associated with P. australis include Proteobacteria, Bacteriodetes, and Firmicutes, Fusobacteria, Actinobacteria, and Planctomycetes families of bacteria among others. Some of these microbes and arbuscular mycorrhizal fungi have facilitated plant growth and phytoremediation by P. australis. This is worthwhile considering that there are vast areas of polluted and wasted land which require reclamation for agricultural use. Common reed with its associated rhizosphere microbes can be utilized in these land reclamation efforts. This present study suggests further work to identify microbes which when administered to P. australis can stimulate its growth in polluted environments and help in land reclamation efforts for agricultural use.

Integration of omics data to unravel root microbiome recruitment

The plant microbiome plays an essential role in supporting plant growth and health, but plant molecular mechanisms underlying its recruitment are still unclear. Multi-omics data integration methods can be used to unravel new signalling relationships. Here, we review the effects of plant genetics and root exudates on root microbiome recruitment, and discuss methodological advances in data integration approaches that can help us to better understand and optimise the crop-microbiome interaction for a more sustainable agriculture.