Shift of bacterial communities in heavy metal-contaminated agricultural land during a remediation process

Anthropogenic-induced environmental and ecological changes in the Nile Delta over the past half-century

Anthropogenic activities over the past half-century have had a negative impact on the wetland ecosystem in the Nile Delta, which provides essential provisioning and regulating services. Therefore, it is crucial to systematically investigate pollution levels and their ecological consequences at both spatial and temporal scales in order to promote sustainable development. In this study, data on metal pollution in the Manzala Lake were compiled through a systematic review of all published literature from 1968 to 2020. Additionally, agricultural data (including land use, pesticide and fertilizer usage, and discharge) and economic data for the same time period were collected to identify the main drivers of pollution. The results indicated an overall increasing trend in heavy metal concentrations during the study period. The average concentrations of metals, arranged in descending order, were as follows: Fe (15,115.5 μg/g) > Mn (722 μg/g) > Zn (115.4 μg/g) > Cu (65.9 μg/g) > Ni (62.5 μg/g) > Cr (58.1 μg/g) > Pb (54.1 μg/g) > Cd (4.7 μg/g) > Hg (0.1 μg/g). A linear regression model revealed that wastewater discharge, water reuse, and the use of pesticides and fertilizers are the main sources of heavy metal pollution in the Manzala Lake. Consequently, there has been a dramatic decrease in the biodiversity of fish and molluscan communities. The study also found a correlation between heavy metal pollution and socio-economic development, highlighting the urgent need for attention to the conservation, management, and sustainable development of the lake.

Influence of conditioner and straw on the herbaceous plant-based phytoremediation copper tailings: a field trial at Liujiagou tailings pond, China

A field trial was performed to carry out an enhanced phytoremediation technique for multi-metal contaminated copper tailings by Sudan grass (Sorghum Sudanese), ryegrass (Lolium perenne L.), and Bermuda grass (Cynodon dactylon), using conditioner (TH-LZ01) and straw combination into composite amendments as soil amendments, aimed to obtain the maximum of phytoremediation effect. The results showed that compared with untreated herbaceous plants, the application of conditioner and straw planted with herbaceous plants reduced the pH and conductivity and increased the organic matter and water content of the copper tailings to different degrees. With the addition of conditioner and straw, the DTPA-Cd, DTPA-Cu, DTPA-Pb, and DTPA-Zn contents in the copper tailings showed a decreasing trend compared with the untreated group. The herbaceous plants were promoted to reduce the percentage contents of acid soluble fractions Cd, Cu, Pb, and Zn and to increase the percentage contents of reducible, oxidizable, and residual fractions heavy metals (Cd, Cu, Pb, and Zn) in the copper tailings to different degrees. The contents of Cd, Cu, Pb, and Zn in the underground part of herbaceous plants were higher than those in the aboveground part, and the contents of Cd, Cu, Pb, and Zn in the aboveground part and underground part decreased after adding conditioner and straw, which indicated that the conditioner and straw inhibited the transport of heavy metals in the plant. Furthermore, the principal component analysis showed that the application of conditioner and straw with planting ryegrass had more potential for improving the physicochemical properties of copper tailings and reducing heavy metal toxicity, followed by Bermuda grass and Sudan grass.

The Potential of Bioaugmentation-Assisted Phytoremediation Derived Maize Biomass for the Production of Biomethane via Anaerobic Digestion

Anthropogenic behaviors are causing the severe build-up of heavy metal (HM) pollutants in the environment, particularly in soils. Amongst a diversity of remediation technologies, phytoremediation is an environmentally friendly technology that, when coupling tolerant plants to selected rhizospheric microorganisms, can greatly stimulate HM decontamination of soils. Maize (Zea mays) is a plant with the reported capacity for HM exclusion from contaminated soil but also has energetic importance. In this study, Zea mays was coupled with Rhizophagus irregularis, an arbuscular mycorrhizal fungus (AMF), and Cupriavidus sp. strain 1C2, a plant growth-promoting rhizobacteria (PGPR), as a remediation approach to remove Cd and Zn from an industrial contaminated soil (1.2 mg Cd kg-1 and 599 mg Zn kg-1) and generate plant biomass, by contrast to the conservative development of the plant in an agricultural (with no metal pollution) soil. Biomass production and metal accumulation by Z. mays were monitored, and an increase in plant yield of ca. 9% was observed after development in the contaminated soil compared to the soil without metal contamination, while the plants removed ca. 0.77% and 0.13% of the Cd and Zn initially present in the soil. The resulting biomass (roots, stems, and cobs) was used for biogas generation in several biomethane (BMP) assays to evaluate the potential end purpose of the phytoremediation-resulting biomass. It was perceptible that the HMs existent in the industrial soil did not hinder the anaerobic biodegradation of the biomass, being registered biomethane production yields of ca. 183 and 178 mL of CH4 g-1 VS of the complete plant grown in non-contaminated and contaminated soils, respectively. The generation of biomethane from HM-polluted soils' phytoremediation-derived maize biomass represents thus a promising possibility to be a counterpart to biogas production in an increasingly challenging status of renewable energy necessities.

Micro/nanoscale bone char alleviates cadmium toxicity and boosts rice growth via positively altering the rhizosphere and endophytic microbial community

This present study investigated pork bone-derived biochar as a promising amendment to reduce Cd accumulation and alleviate Cd-induced oxidative stress in rice. Micro/nanoscale bone char (MNBC) pyrolyzed at 400 °C and 600 °C was synthesized and characterized before use. The application rates for MNBCs were set at 5 and 25 g·kg^-1 and the Cd exposure concentration was 15 mg·kg^-1. MNBCs increased rice biomass by 15.3-26.0% as compared to the Cd-alone treatment. Both types of MNBCs decreased the bioavailable Cd content by 27.4-54.8%; additionally, the acid-soluble Cd fraction decreased by 10.0-12.3% relative to the Cd alone treatment. MNBC significantly reduced the cell wall Cd content by 50.4-80.2% relative to the Cd-alone treatment. TEM images confirm the toxicity of Cd to rice cells and that MNBCs alleviated Cd-induced damage to the chloroplast ultrastructure. Importantly, the addition of MNBCs decreased the abundance of heavy metal tolerant bacteria, Acidobacteria and Chloroflexi, by 29.6-41.1% in the rhizosphere but had less impact on the endophytic microbial community. Overall, our findings demonstrate the significant potential of MNBC as both a soil amendment for heavy metal-contaminated soil remediation and for crop nutrition in sustainable agriculture.

Effect of composite amendments on physicochemical properties of copper tailings repaired by herbaceous plants

Phytoremediation is considered to be the most environmentally friendly green restoration technology for dealing with mine waste. Adding amendments can improve the substrate environment for plant growth and enhance remediation efficiency. Herbaceous plants have become the preferred species for vegetation restoration in abandoned mines because of their fast greening and simple management. After 8 weeks of pot experiments in the early stage, it was shown that the plant height and fresh weight of the plants treated with 5% conditioner and 0.5% straw (C₂S₂) were significantly higher than those of other treatments. Considering that, in this paper, to explore the effect of composite amendments on physicochemical properties of copper tailings repaired by herbaceous plants, the untreated copper tailings were employed as the control group, whereas copper tailings repaired by ryegrass (Lolium perenne L.), vetiver grass (Chrysopogon zizanioides L.), and tall fescue (Festuca arundinacea) with or without conditioners and straw combination into the compound amendments were taken separately as the test group. After 6 months of planting, the pH, electrical conductivity, water content, available potassium, organic matter, total nitrogen, and available phosphorus in the main physical and chemical properties of copper tailings in each experimental area were analyzed. The results showed that the electrical conductivity, organic matter, and total nitrogen content of copper tailings were improved to a certain extent by planting plants without treatment. Meanwhile, compared with the control group, all indexes of planting plants showed an upward trend after adding composite amendments. Among them, pH, water content, and available potassium content of copper tailings were enhanced more obviously. Furthermore, as discovered from the gray correlation analysis results, vetiver grass planted with composite amendments has the best comprehensive effect of improving the physicochemical properties of copper tailings, followed by tall fescue and ryegrass.

Response mechanisms of bacterial communities and nitrogen cycle functional genes in millet rhizosphere soil to chromium stress

Introduction

A growing amount of heavy metal contamination in soil disturbs the ecosystem's equilibrium, in which microbial populations play a key role in the nutrient cycle of soils. However, given the different sensitivity of microbial communities to different spatial and temporal scales, microbial community structure and function also have varied response mechanisms to different heavy metal contaminated habitats.

Methods

In this study, samples were taken prior to Cr stress (CK) and 6 h and 6 days after Cr stress (Cr_6h, Cr_6d) in laboratory experiments. High-throughput sequencing revealed trends in the structure and diversity of the bacterial communities, and real-time fluorescence quantitative polymerase chain reaction (qPCR) was used to analyze trends in nitrogen cycle functional genes (AOA-amoA, AOB-amoA, narG, nirK, and nifH).

Results

The findings showed that (1) the composition structure of the soil bacterial community changed considerably in Cr-stressed soils; α-diversity showed significant phase transition characteristic from stress to stability (p < 0.05). (2) With an overall rising tendency, the abundance of the nitrogen cycle functional genes (AOA-amoA and AOB-amoA) decreased considerably before increasing, and α-diversity dramatically declined (p < 0.05). (3) The redundancy analysis (RDA) and permutational multivariate analysis of variance (PERMANOVA) tests results showed that the soil physicochemical parameters were significantly correlated with the nitrogen cycle functional genes (r: 0.4195, p < 0.01). Mantel analysis showed that available nitrogen (N), available potassium (K), and available phosphorus (P) were significantly correlated with nifH (p = 0.006, 0.008, 0.004), and pH was highly significantly correlated with nifH (p = 0.026). The PLS-ME (partial least squares path model) model further demonstrated a significant direct effect of the soil physicochemical parameters on the nitrogen cycling functional genes.

Discussion

As a result, the composition and diversity of the bacterial community and the nitrogen cycle functional genes in Cr-stressed agricultural soils changed considerably. However, the influence of the soil physicochemical parameters on the functional genes involved in the nitrogen cycle was greater than that of the bacterial community. and Cr stress affects the N cycling process in soil mainly by affecting nitrification. This research has significant practical ramifications for understanding the mechanisms of microbial community homeostasis maintenance, nitrogen cycle response mechanisms, and soil remediation in heavy metal-contaminated agricultural soils.

Silicon and soil microorganisms improve rhizospheric soil health with bacterial community, plant growth, performance and yield

The interaction of silicon and soil microorganisms stimulates crop enhancement to ensure sustainable agriculture. Silicon may potentially increase nutrient availability in rhizosphere with improved plants' growth, development as it does not produce phytotoxicity. The rhizospheric microbiome accommodates a variety of microbial species that live in a small area of soil directly associated with the hidden half plants' system. Plant growth-promoting rhizobacteria (PGPR) play a major role in plant development in response to adverse climatic conditions. PGPRs may enhance the growth, quality, productivity in variety of crops, and mitigate abiotic stresses by reprogramming stress-induced physiological variations in plants via different mechanisms, such as synthesis of indole-3-acetic acid, 1-aminocyclopropane-1-carboxylate deaminase, exopolysaccharides, volatile organic compounds, atmospheric nitrogen fixation, and phosphate solubilization. Our article eye upon interactions of silicon and plant microbes which seems to be an opportunity for sustainable agriculture for series of crops and cropping systems in years to come, essential to safeguard the food security for masses.

Diversity and functional traits of indigenous soil microbial flora associated with salinity and heavy metal concentrations in agricultural fields within the Indus Basin region, Pakistan

Soil salinization and heavy metal (HM) contamination are major challenges facing agricultural systems worldwide. Determining how soil microbial communities respond to these stress factors and identifying individual phylotypes with potential to tolerate these conditions while promoting plant growth could help prevent negative impacts on crop productivity. This study used amplicon sequencing and several bioinformatic programs to characterize differences in the composition and potential functional capabilities of soil bacterial, fungal, and archaeal communities in five agricultural fields that varied in salinity and HM concentrations within the Indus basin region of Pakistan. The composition of bacteria with the potential to fix atmospheric nitrogen (N) and produce the enzyme 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase were also determined. Microbial communities were dominated by: Euryarchaeota (archaea), Actinobacteria, Proteobacteria, Planctomycetota, Firimicutes, Patescibacteria and Acidobacteria (bacteria), and Ascomycota (fungi), and all soils contained phylotypes capable of N-fixation and ACC-deaminase production. Salinity influenced bacterial, but not archaeal or fungal communities. Both salinity and HM altered the relative abundance of many phylotypes that could potentially promote or harm plant growth. These stress factors also appeared to influence the potential functional capabilities of the microbial communities, especially in their capacity to cycle phosphorous, produce siderophores, and act as symbiotrophs or pathotrophs. Results of this study confirm that farms in this region are at risk due to salinization and excessive levels of some toxic heavy metals, which could negatively impact crop and human health. Changes in soil microbial communities and their potential functional capabilities are also likely to affect several critical agroecosystem services related to nutrient cycling, pathogen suppression, and plant stress tolerance. Many potentially beneficial phylotypes were identified that appear to be salt and HM tolerant and could possibly be exploited to promote these services within this agroecosystem. Future efforts to isolate these phylotypes and determine whether they can indeed promote plant growth and/or carry out other important soil processes are recommended. At the same time, identifying ways to promote the abundance of these unique phylotypes either through modifying soil and crop management practices, or developing and applying them as inoculants, would be helpful for improving crop productivity in this region.

Profile of Bacterial Community and Antibiotic Resistance Genes in Typical Vegetable Greenhouse Soil

The use of vegetable greenhouse production systems has increased rapidly because of the increasing demand for food materials. The vegetable greenhouse production industry is confronted with serious environmental problems, due to their high agrochemical inputs and intensive utilization. Besides this, antibiotic-resistant bacteria, carrying antibiotic-resistance genes (ARGs), may enter into a vegetable greenhouse with the application of animal manure. Bacterial communities and ARGs were investigated in two typical vegetable-greenhouse-using counties with long histories of vegetable cultivation. The results showed that Proteobacteria, Firmicutes, Acidobacteria, Chloroflexi, and Gemmatimonadetes were the dominant phyla, while aadA, tetL, sul1, and sul2 were the most common ARGs in greenhouse vegetable soil. Heatmap and principal coordinate analysis (PCoA) demonstrated that the differences between two counties were more significant than those among soils with different cultivation histories in the same county, suggesting that more effects on bacterial communities and ARGs were caused by soil type and manure type than by the accumulation of cultivation years. The positive correlation between the abundance of the intI gene with specific ARGs highlights the horizontal transfer potential of these ARGs. A total of 11 phyla were identified as the potential hosts of specific ARGs. Based on redundancy analysis (RDA), Ni and pH were the most potent factors determining the bacterial communities, and Cr was the top factor affecting the relative abundance of the ARGs. These results might be helpful in drawing more attention to the risk of manure recycling in the vegetable greenhouse, and further developing a strategy for practical manure application and sustainable production of vegetable greenhouses.

Plants-Microorganisms-Based Bioremediation for Heavy Metal Cleanup: Recent Developments, Phytoremediation Techniques, Regulation Mechanisms, and Molecular Responses

Rapid industrialization, mine tailings runoff, and agricultural activities are often detrimental to soil health and can distribute hazardous metal(loid)s into the soil environment, with harmful effects on human and ecosystem health. Plants and their associated microbes can be deployed to clean up and prevent environmental pollution. This green technology has emerged as one of the most attractive and acceptable practices for using natural processes to break down organic contaminants or accumulate and stabilize metal pollutants by acting as filters or traps. This review explores the interactions between plants, their associated microbiomes, and the environment, and discusses how they shape the assembly of plant-associated microbial communities and modulate metal(loid)s remediation. Here, we also overview microbe-heavy-metal(loid)s interactions and discuss microbial bioremediation and plants with advanced phytoremediation properties approaches that have been successfully used, as well as their associated biological processes. We conclude by providing insights into the underlying remediation strategies' mechanisms, key challenges, and future directions for the remediation of metal(loid)s-polluted agricultural soils with environmentally friendly techniques.

Nanotechnology in the Restoration of Polluted Soil

The advancements in nanoparticles (NPs) may be lighting the sustainable and eco-friendly path to accelerate the removal of toxic compounds from contaminated soils. Many efforts have been made to increase the efficiency of phytoremediation, such as the inclusion of chemical additives, the application of rhizobacteria, genetic engineering, etc. In this context, the integration of nanotechnology with bioremediation has introduced new dimensions for revamping the remediation methods. Hence, advanced remediation approaches combine nanotechnological and biological remediation methods in which the nanoscale process regulation supports the adsorption and deterioration of pollutants. Nanoparticles absorb/adsorb a large variety of contaminants and also catalyze reactions by lowering the energy required to break them down, owing to their unique surface properties. As a result, this remediation process reduces the accumulation of pollutants while limiting their spread from one medium to another. Therefore, this review article deals with all possibilities for the application of NPs for the remediation of contaminated soils and associated environmental concerns.

Co-occurrence Interaction Networks of Extremophile Species Living in a Copper Mining Tailing

Copper mining tailings are characterized by high concentrations of heavy metals and an acidic pH, conditions that require an extreme adaptation for any organism. Currently, several bacterial species have been isolated and characterized from mining environments; however, very little is known about the structure of microbial communities and how their members interact with each other under the extreme conditions where they live. This work generates a co-occurrence network, representing the bacterial soil community from the Cauquenes copper tailing, which is the largest copper waste deposit worldwide. A representative sampling of six zones from the Cauquenes tailing was carried out to determine pH, heavy metal concentration, total DNA extraction, and subsequent assignment of Operational Taxonomic Units (OTUs). According to the elemental concentrations and pH, the six zones could be grouped into two sectors: (1) the "new tailing," characterized by neutral pH and low concentration of elements, and (2) the "old tailing," having extremely low pH (~3.5) and a high concentration of heavy metals (mainly copper). Even though the abundance and diversity of species were low in both sectors, the Pseudomonadaceae and Flavobacteriaceae families were over-represented. Additionally, the OTU identifications allowed us to identify a series of bacterial species with diverse biotechnological potentials, such as copper bioleaching and drought stress alleviation in plants. Using the OTU information as a template, we generated co-occurrence networks for the old and new tailings. The resulting models revealed a rearrangement between the interactions of members living in the old and new tailings, and highlighted conserved bacterial drivers as key nodes, with positive interactions in the network of the old tailings, compared to the new tailings. These results provide insights into the structure of the soil bacterial communities growing under extreme environmental conditions in mines.

Heavy Metals and Human Health: Possible Exposure Pathways and the Competition for Protein Binding Sites

Heavy metals enter the human body through the gastrointestinal tract, skin, or via inhalation. Toxic metals have proven to be a major threat to human health, mostly because of their ability to cause membrane and DNA damage, and to perturb protein function and enzyme activity. These metals disturb native proteins’ functions by binding to free thiols or other functional groups, catalyzing the oxidation of amino acid side chains, perturbing protein folding, and/or displacing essential metal ions in enzymes. The review shows the physiological and biochemical effects of selected toxic metals interactions with proteins and enzymes. As environmental contamination by heavy metals is one of the most significant global problems, some detoxification strategies are also mentioned.