Soil Microbial Diversity in Relation to Heavy Metals

The Marine-Origin Exopolysaccharide-Producing Bacteria Micrococcus Antarcticus HZ Inhibits Pb Uptake in Pakchoi (Brassica chinensis L.) and Affects Rhizosphere Microbial Communities

Exopolysaccharides (EPSs) produced by microorganisms play an important role in biotolerance and reducing heavy metal (HM) contamination by limiting the migration of HMs into plants. However, research on the application of EPS-producing marine bacteria for soil heavy metal remediation remains limited, particularly regarding their mechanisms of HM immobilization in soil and impact on plant growth. In this study, the EPS-producing marine bacterium Micrococcus antarcticus HZ was investigated for its ability to immobilize Pb and produce EPSs in soil filtrate. The effects on the growth quality and biomass of pakchoi (Brassica chinensis L.), as well as bacterial communities in inter-root soil contaminated with Pb, were also investigated. The results indicated that HZ could reduce the Pb concentration in the soil filtrate, achieving a removal rate of 43.25-63.5%. The EPS content and pH levels increased in the presence of Pb. Pot experiments showed that adding HZ significantly increased the biomass of pakchoi (9.45-14.69%), vitamin C (Vc) (9.69-12.92%), and soluble protein content (22.58-49.7%). HZ reduced the Pb content in the roots (17.52-47.48%) and leaves (edible tissues) (43.82-52.83%) of pakchoi. HZ increased soil enzyme activities (alkaline phosphatase, dehydrogenase, and urease), and the contents of ammonium nitrogen and nitrate nitrogen. Additionally, HZ also increased the relative abundance of beneficial bacteria (e.g., Proteobacteria, Cyanobacteria, and Chlorobacteria) in the inter-root soil, which have prophylactic and heavy-metal fixation functions. In summary, HZ reduces effective Pb content in edible tissues, roots, and inter-root soil by regulating inter-root soil microbial community structure, increasing soil pH, nitrogen content, and soil enzyme activity, and altering dominant phylum abundance.

Toxicity factors to assess the ecological risk for soil microbial communities

The toxicity factor (TF), a critical parameter within the potential ecological risk index (RI), is determined without accounting for microbial factors. It is considerable uncertainty exists concerning its validity for quantitatively assessing the influence of metal(loid)s on microorganisms. To evaluate the suitability of TF, we constructed microcosm experiments with varying RI levels (RI = 100, 200, 300, 500, and 700) by externally adding zinc (Zn), chromium (Cr), copper (Cu), lead (Pb), nickel (Ni), cadmium (Cd), and mercury (Hg) to uncontaminated soil (CK). Quantitative real-time PCR (qPCR) and high-throughput sequencing techniques were employed to measure the abundance and community of bacteria and fungi, and high-throughput qPCR was utilised to quantify functional genes associated with CNPS cycles. The results demonstrated that microbial diversity and function exhibited significant alterations (p < 0.05) in response to increasing RI levels, and the influences on microbial community structure, enzyme activity, and functional gene abundances were different due to the types of metal(loid)s treatments. At the same RI level, significant differences (p < 0.05) were discerned in microbial diversity and function across metal(loid) treatments, and these differences became more pronounced (p < 0.001) at higher levels. These findings suggest that TF may not be suitable for the quantitative assessment of microbial ecological risk. Therefore, we adjusted the TF by following three steps (1) determining the adjustment criteria, (2) deriving the initial TF, and (3) adjusting and optimizing the TF. Ultimately, the optimal adjusted TF was established as Zn = 1.5, Cr = 4.5, Cu = 6, Pb = 4.5, Ni = 5, Cd = 22, and Hg = 34. Our results provide a new reference for quantitatively assessing the ecological risks caused by metal(loid)s to microorganisms.

Assessing heavy metal contamination in Amomum villosum Lour. fruits from plantations in Southern China: Soil-fungi-plant interactions

Amomum villosum Lour. fruit is a common healthy food widely cultivated in southern China. Heavy metal contamination of farmland soils has becomes a serious environmental concern in China. Heavy metals in soil can be introduced into the food chain and pose health risks to humans. However, microbial communities may play beneficial roles in plants grown in metal-polluted soils. This study aimed to assess the potential health risks of heavy metals in soils and A. villosum fruits from different production areas and to explore the soil-microbe-plant regulation pattern for heavy metals in A. villosum fruits. Soil and A. villosum fruit samples were collected from nine planting fields in four provinces of southern China. The results showed that soils from seven areas were polluted with heavy metals to different degrees. Cr and Mn were the most serious contaminating elements. However, the accumulation of heavy metals in A. villosum fruit was negligible with no expected human health risks. Partial least squares path analysis of structural equation modeling showed that the accumulation of heavy metals in A. villosum fruits was influenced by multiple factors. More importantly, the PLS-SEM revealed that the heavy metal content in A. villosum fruits was indirectly affected by soil heavy metals through the regulation of the microbial community. Furthermore, some fungal phyla (e.g., Ascomycota and Chytridiomycota) and genera (e.g., Mucor) were related to the heavy metal content in the soil and in A. villosum fruits. The results of this study verified that soil fungal community play an important role in the accumulation of heavy metals in A. villosum fruits. Using fungi provides a potential biological strategy for reducing the health risk posed by heavy metals in food.

Microbiological status of natural and anthropogenic soils of the Taganrog Bay coast at different levels of combined pollution with heavy metals and PAHs

The effect of heavy metals (HMs) and polycyclic aromatic hydrocarbons (PAHs) pollution on the microbiological status of soils on the coast of the Taganrog Bay and adjacent areas was studied. The content of total and exchangeable forms of HMs, the content of 16 priority PAHs and the abundance of several groups of culturable microorganisms was determined, namely copiotrophic, prototrophic, aerobic spore-forming bacteria, actinomycetes, molds and yeasts. The content of total and exchangeable forms of HMs in urban coastal soils in industrial zone significantly exceeded that in non-urban soils. The maximum concentrations of total forms of Mn, Cr, Ni, Cu, Zn, Pb and Cd are 1821, 871, 143, 89, 1390, 317 and 10 mg/kg, respectively. The median value of the total content of 16 PAHs in urban soils is 3 times higher than in the soils of natural areas and reached 4309 ng/g. The lowest numbers of copiotrophic bacteria, prototrophic bacteria and aerobic spore-forming bacteria were found in the soils of industrial zone: 6.8, 13.8 and 0.63 million CFU g-1 dry soil, respectively. The largest numbers of copiotrophic bacteria, prototrophic bacteria and aerobic spore-forming bacteria were recorded in the soils of natural areas-72.5, 136 and 5.73 million CFU g-1 dry soil, respectively. It was found that the abundance of copiotrophs, prototrophs, and aerobic spore-forming bacteria is more affected by the urbanization of coastal soils including the pollution of HMs and PAHs. Other groups of microorganisms (actinomycetes, molds and yeasts) turned out to be more resistant to anthropogenic factors.

Microbial communities in tree root-compartment niches under Cd and Zn pollution: Structure, assembly process and co-occurrence relationship

Woody plants have showed great potential in remediating severely contaminated soils by heavy metals (HMs) due to their cost-efficient and ecologically friendly trait. It is believed the root-associated microbiota plays a vital role in phytoremediation for HMs. However, the ecological process controlling the assembly and composition of tree root-associated microbial communities under HMs stress remains poorly understood. Herein, we profiled the bulk soil, rhizosphere and endosphere microbial communities of trees growing in heavily Cd and Zn polluted soil. The microbiota was gradually filtered from bulk soil to the tree roots and was selectively enriched in roots with specific taxa, such as Proteobacteria and Ascomycota. The microbial community assembly along the soil-root continuum was mainly controlled by deterministic processes from bulk soil to the endosphere, with the normalized stochasticity ratio (NST) indices of 67.16-31.05 % and 30.37-15.02 % for bacteria and fungi, respectively. Plant selection pressure sequentially increased from bulk soil to rhizosphere to endosphere, with the reduced bacterial alpha diversity accompanying the consequently reduced complexity of the co-occurrence network. Together, the findings provide new evidence for horizontal transmission of endophytic microbiome from soil to the host, which can shed light on the future screening and application of microbial-assisted phytoremediation.

Dynamic analysis of the microbial communities and metabolome of healthy banana rhizosphere soil during one growth cycle

Background

The banana-growing rhizosphere soil ecosystem is very complex and consists of an entangled network of interactions between banana plants, microbes and soil, so identifying key components in banana production is difficult. Most of the previous studies on these interactions ignore the role of the banana plant. At present, there is no research on the the micro-ecological environment of the banana planting growth cycle.

Methods

Based on high-throughput sequencing technology and metabolomics technology, this study analyzed the rhizosphere soil microbial community and metabolic dynamics of healthy banana plants during one growth cycle.

Results

Assessing the microbial community composition of healthy banana rhizosphere soil, we found that the bacteria with the highest levels were Proteobacteria, Chloroflexi, and Acidobacteria, and the dominant fungi were Ascomycota, Basidiomycota, and Mortierellomycota. The metabolite profile of healthy banana rhizosphere soil showed that sugars, lipids and organic acids were the most abundant, accounting for about 50% of the total metabolites. The correlation network between fungi and metabolites was more complex than that of bacteria and metabolites. In a soil environment with acidic pH, bacterial genera showed a significant negative correlation with pH value, while fungal genera showed no significant negative correlation with pH value. The network interactions between bacteria, between fungi, and between bacteria and fungi were all positively correlated.

Conclusions

Healthy banana rhizosphere soil not only has a stable micro-ecology, but also has stable metabolic characteristics. The microorganisms in healthy banana rhizosphere soil have mutually beneficial rather than competitive relationships.

Application of cotton straw biochar and compound Bacillus biofertilizer decrease the bioavailability of soil cd through impacting soil bacteria

Background

Cd seriously threatens soil environment, remedying Cd in farmland and clearing the response of soil environment to modifiers in Cd-contaminated soils is necessary. In this study, the effects of cotton straw biochar and compound Bacillus biofertilizer used as modifiers on the biochemical properties, enzyme activity, and microbial diversity in Cd-contaminated soils (1, 2, and 4 mg·kg⁻¹) were investigated.

Results

The results showed that both cotton straw biochar and compound Bacillus biofertilizer could improve the soil chemical characteristics, including the increase of soil C/N ratio, electrical conductance (EC) and pH, and the most important decrease of soil available Cd content by 60.24% and 74.34%, respectively (P < 0.05). On the other hand, adding cotton straw biochar and compound Bacillus biofertilizer in Cd stressed soil also improved soil biological characteristics. Among them, cotton straw biochar mainly through increasing soil alkaline phosphatase activity and improve bacteria abundance, compound Bacillus biofertilizer by increasing soil invertase, alkaline phosphatase, catalase, and urease activity increased bacterial community diversity. On the whole, the decrease of soil available Cd was mainly caused by the increase of soil pH, C/N, urease and alkaline phosphatase activities, and the relative abundance of Acidobacteria and Proteobacteria.

Conclusions

In summary, the applications of cotton straw biochar and compound Bacillus biofertilizer could decrease soil available Cd concentration, increase soil bacterial community diversity and functions metabolism, and reduce the damage of Cd stress, compared with cotton straw biochar, compound Bacillus biofertilizer was more effective in immobilizing Cd and improving soil environmental quality.

Differential strategies of two species of arbuscular mycorrhizal fungi in the protection of maize plants grown in chromium-contaminated soils

Chromium (Cr) is a nonessential element for plants that is extremely toxic at high concentrations. Zea mays L. is a species of plant that has developed adaptive mechanisms to increase its tolerance and absorption capacity for this metal. One effective mechanism is to form associations with arbuscular mycorrhizal fungi (AMF), which help the plant cope with stress from heavy metals such as Cr. However, it is still not clear which species of AMF are more efficient as bioremediating agents for plants of agricultural importance. Here, we evaluated the effect of Gigaspora gigantea and Rhizophagus irregularis as protective agents of maize plants in soils contaminated with Cr at concentrations of 0, 48.5, 97 and 194 mg kg^-1 under greenhouse conditions. Maize tolerance to Cr was corroborated, as well as increased absorption of this element by plants associated with both species of AMF. G. gigantea caused an increase in nitrogen content and greater translocation of Cr to the aerial part of the plant; R. irregularis registered an increase in the formation of arbuscules and vesicles with increasing metal concentration and greater retention of Cr in the roots of the plants. Based on these results, we can conclude that the analyzed species of fungi use different strategies, with similar effectiveness, to enhance the absorption capacity of Cr by the plant and influence the differential deposition of this metal in various parts of the plant.

Bio-indicators in cadmium toxicity: Role of HSP27 and HSP70

Heat shock proteins (HSPs) are a family of proteins that are expressed by cells in reply to stressors. The changes in concentration of HSPs could be utilized as a bio-indicator of oxidative stress caused by heavy metal. Exposure to the different heavy metals may induce or reduce the expression of different HSPs. The exposure to cadmium ion (Cd²⁺) could increase HSP70 and HSP27 over 2- to 10-fold or even more. The in vitro and in vivo models indicate that the HSP70 family is more sensitive to Cd intoxication than other HSPs. The analyses of other HSPs along with HSP70, especially HSP27, could also be useful to obtain more accurate results. In this regard, this review focuses on examining the literature to bold the futuristic uses of HSPs as bio-indicators in the initial assessment of Cd exposure risks in defined environments.

A comprehensive survey on the horizontal and vertical distribution of heavy metals and microorganisms in soils of a Pb/Zn smelter

Smelter emissions have brought serious heavy metal contamination. Comprehensive surveys of spatial heavy metal and microorganism distribution in soils of smelters aera are still limited. In this study, the horizontal and vertical profiles of heavy metals as well as microorganisms of 80 samples from 5 soil layers of 16 sites in a Pb/Zn smelter were studied. Pollution index indicated the pollution level as Cd > Zn > Pb > As > Cu > Mn > Co > Cr > V, and the severe pollutants were Cd, Zn, Pb, As and Cu. The hazard quotient and hazard index indicated that the topsoil might pose high chronic risk to children mainly due to high content of Pb, As and Cd. The whole smelter was heavily polluted even to the depth of 100 cm as revealed by Nemerow pollution indices. Depth-related microbiota analysis indicated high richness of indigenous microorganisms and significant differences in vertical microbial structure. Proteobacteria was the dominant phylum in all depth layers, followed by Firmicutes, Actinobacteria, Bacteroidetes and Acidobacteria as major phyla. pH and heavy metals Zn, Cu, As, Mn and Cd significantly influenced the microbiota composition. Metagenomic functional prediction suggested antioxidant response, metal exportation and biotransformation play roles in bio-resistance to and bioremoval of heavy metals.

Unravelling the antibiotic and heavy metal resistome of a chronically polluted soil

The antibiotic and heavy metal resistome of a chronically polluted soil (3S) obtained from an automobile workshop in Ilorin, Kwara State, Nigeria was deciphered via functional annotation of putative ORFs (open reading frames). Functional annotation of antibiotic and heavy metal resistance genes in 3S metagenome was conducted using the Comprehensive Antibiotic Resistance Database (CARD), Antibiotic Resistance Gene-annotation (ARG-ANNOT) and Antibacterial Biocide and Metal Resistance Gene Database (BacMet). Annotation revealed detection of resistance genes for 15 antibiotic classes with the preponderance of beta lactamases, mobilized colistin resistance determinant (mcr), glycopepetide and tetracycline resistance genes, the OqxBgb and OqxA RND-type multidrug efflux pumps, among others. The dominance of resistance genes for antibiotics effective against members of the Enterobacteriaceae indicate possible contamination with faecal materials. Annotation of heavy metal resistance genes revealed diverse resistance genes responsible for the uptake, transport, detoxification, efflux and regulation of copper, zinc, cadmium, nickel, chromium, cobalt, mercury, arsenic, iron, molybdenum and several others. Majority of the antibiotic and heavy metal resistance genes detected in this study are borne on mobile genetic elements, which facilitate their spread and dissemination in the polluted soil. The presence of the heavy metal resistance genes is strongly believed to play a major role in the proliferation of antibiotic resistance genes. This study has established that soil is a huge repertoire of antibiotic and heavy metal resistome and due to the intricate link between human, animals and the soil environment, it may be a major contributor to the proliferation of multidrug-resistant clinical pathogens.

Advances in monitoring soil microbial community dynamic and function

Microorganisms are vital to the overall ecosystem functioning, stability, and sustainability. Soil fertility and health depend on chemical composition and also on the qualitative and quantitative nature of microorganisms inhabiting it. Historically, denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE), single-strand conformation polymorphism, DNA amplification fingerprinting, amplified ribosomal DNA restriction analysis, terminal restriction fragment length polymorphism, length heterogeneity PCR, and ribosomal intergenic spacer analysis were used to assess soil microbial community structure (SMCS), abundance, and diversity. However, these methods had significant shortcomings and limitations for application in land reclamation monitoring. SMCS has been primarily determined by phospholipid fatty acid (PLFA) analysis. This method provides a direct measure of viable biomass in addition to a biochemical profile of the microbial community. PLFA has limitations such as overlap in the composition of microorganisms and the specificity of PLFAs signature. In recent years, high-throughput next-generation sequencing has dramatically increased the resolution and detectable spectrum of diverse microbial phylotypes from environmental samples and it plays a significant role in microbial ecology studies. Next-generation sequencings using 454, Illumina, SOLiD, and Ion Torrent platforms are rapid and flexible. The two methods, PLFA and next-generation sequencing, are useful in detecting changes in microbial community diversity and structure in different ecosystems. Single-molecule real-time (SMRT) and nanopore sequencing technologies represent third-generation sequencing (TGS) platforms that have been developed to address the shortcomings of second-generation sequencing (SGS). Enzymatic and soil respiration analyses are performed to further determine soil quality and microbial activities. Other valuable methods that are being recently applied to microbial function and structures include NanoSIM, GeoChip, and DNA stable staple isotope probing (DNA-SIP) technologies. They are powerful metagenomics tool for analyzing microbial communities, including their structure, metabolic potential, diversity, and their impact on ecosystem functions. This review is a critical analysis of current methods used in monitoring soil microbial community dynamic and functions.

Metal Toxicity and Resistance in Plants and Microorganisms in Terrestrial Ecosystems

Metals are major abiotic stressors of many organisms, but their toxicity in plants is not as studied as in microorganisms and animals. Likewise, research in plant responses to metal contamination is sketchy. Candidate genes associated with metal resistance in plants have been recently discovered and characterized. Some mechanisms of plant adaptation to metal stressors have been now decrypted. New knowledge on microbial reaction to metal contamination and the relationship between bacterial, archaeal, and fungal resistance to metals has broadened our understanding of metal homeostasis in living organisms. Recent reviews on metal toxicity and resistance mechanisms focused only on the role of transcriptomics, proteomics, metabolomics, and ionomics. This review is a critical analysis of key findings on physiological and genetic processes in plants and microorganisms in responses to soil metal contaminations.