Atmospheric Deposition-Carried Zn and Cd from a Zinc Smelter and Their Effects on Soil Microflora as Revealed by 16S rDNA

The concentrations of microelements in forest mushrooms are influenced by soil pH and C/N ratio and less by stand characteristics

The fruitbodies or sporocarps formed by mushrooms can accumulate mineral elements, such as selenium, zinc or copper, making them an important source of micronutrients essential to humans. However, the literature about environmental factors affecting mineral composition in mushrooms is scarce and limited to the ambiguous impact of soil properties and region. In our study, we investigated the effects of tree stand characteristics (tree species and tree canopy cover), understory cover, and soil properties (pH and C/N ratio of the soil) on the concentration of minerals in six edible mushroom species: Laccaria laccata, L. proxima, L. amethystina, Lepista nuda, Lycoperdon perlatum, and Calvatia excipuliformis, collected on 20 plots covered by stands of different tree species composition and varying in the understory cover. We estimated the concentration of eight elements (Zn, Se, Mg, Mn, Cu, Co, Cr, Mo) using the ICP-MS (Inductively Coupled Plasma - Mass Spectrometry) technique and compared their concentration between the plots, using ordination and linear regression methods. Our research revealed that mushroom species identity, including its ecological role and phylogenetic affinity, had the greatest effect on the mineral composition of mushrooms. The effect of environmental factors depended also on the micronutrient identity. Some elements were not affected at all (Co, Cr), some only by soil reaction or C/N ratio (Mn, Mg, Cu), while others were influenced by both tree stand characteristics and soil properties (Se, Zn, Mo). This knowledge enables us to maximize the content of minerals in harvested mushrooms by collecting them in specific areas. For example, mushrooms, which are sources of Se and Zn, can be gathered in coniferous forests characterized by acid soils, low canopy cover, and minimal understory cover. This targeted collection approach can effectively increase the mineral content in harvested mushrooms, thereby enhancing their health benefits.

Roots recruited distinct rhizo-microbial communities to adapt to long-term Cd and As co-contaminated soil in wheat-maize rotation

Cd and As accumulation in staple crops poses potential risks to food safety and human health. Rhizo-microbial communities are involved in their behaviors from soil to crops. However, the responses of rhizo-microbial communities to different Cd and As co-contaminated soils in wheat‒maize rotation are still unclear. This study explored whether wheat or maize could recruit distinct rhizo-microbial communities to adapt to long-term co-contaminated soils with low or high levels of Cd and As (LS or HS). It was apparent that the average wheat grain-Cd/As concentrations were 17.96-fold/4.81-fold in LS and 5.64-fold/7.70-fold in HS higher than those in maize grains, significantly depending on the mobility of Cd/As in soil-crop system, especially from soil to root and from straw to grain. Meanwhile, wheat or maize roots recruited specific bacteria and fungi in LS and HS, which were substantially associated with Cd/As bioavailability in rhizosphere. Wheat roots recruited specific bacterial genera norank_c__MB-A2-108 (Actinobacteria), norank_f__JG30-KF-CM45 (Chloroflexi), and norank_o__Rokubacteriales (Methylomirabilota) and fungal genera Metarhizium and Olpidium under HS, and their relative abundances were positively correlated with soil Cd/As bioavailability and were resistant to Cd and As co-contamination. However, bacterial genera Arthrobacter, Nocardioides, Devosia, Skermanella, and Pedobacter were sensitive to Cd and As co-contamination and were specifically enriched in wheat rhizospheres under LS. Meanwhile, the bacterial genus norank_c__KD4-96 (Chloroflexi) was resistant to Cd and As co-contamination under HS and was distinctly enriched in maize rhizosphere. Furthermore, the roots of wheat and maize recruited the bacterial genus Marmoricola in LS, which was sensitive to Cd and As co-contamination, and recruited specific fungal genus Fusicolla in HS, which was tolerant to Cd and As co-contamination. These results confirmed that HS and LS shifted the composition and structure of the rhizo-microbial communities in the wheat-maize rotation to promote crops survival in different long-term Cd and As co-contaminated soils.

Differential response of the soil nutrients, soil bacterial community structure and metabolic functions to different risk areas in Lead-Zine tailings

Rapid growth in the mining industry has brought about a large formation of tailings, which result in serious destruction of the ecological environment and severe soil pollution problems. This study assesses soil nutrients, soil bacterial community and soil microbes' metabolic function in heavily polluted areas (W1), moderately polluted areas (W2), lightly polluted areas (W3) and clean areas (CK) using 16S Illumina sequencing. The results of this study showed that compared with CK, a severe loss of soil nutrients and richness of OTUs (Chao1 and ACE indices) were observed with the aggravated pollution of tailings. The Chao1 and ACE indices in the W1 group decreased significantly by 15.53 and 16.03%, respectively, (p < 0.01). Besides, the relative abundance of Actinobacteria and Proteobacteria was high whereas and relative abundance of Chloroflexi in the polluted areas. Among them, W1 groups increased significantly the relative abundance of Actinobacteria and decreased significantly the relative abundance of Chloroflexi, these can be used as indicator phyla for changes in soil community structures under polluted stress. Tax4 Fun analysis showed that W1 groups affected the soil bacterial community and altered the primary types of biological metabolism in polluted areas. Tailings have adverse impacts on soil bacterial community and metabolic functions, and the deterioration in soil quality is dependent on the levels of tailings pollution. Cumulatively, this study provides valuable information on the bacterial community structure and metabolic functions in the tailing polluted soil.

Heavy Metals Contained Within a Pb-Zn Waste Heap Exhibit Selective Association with Microbial Modules as Revealed by Network Analysis

Heavy metal contamination is a global environmental concern due to its persistence and toxicity. To explore soil microbial interaction mechanisms and their association with heavy metals on a Pb-Zn waste heap, ecological network analysis tools were used to analyze high-throughput data in microbiology. The microbial network was divided into several modules, but heavy metals were associated with specific modules. The heavy metal-tolerant module (M2) had a more negative than positive relationship with the heavy metal-mid-tolerant modules (M1 and M3). Tight coupling between fungal and bacterial operational taxonomic units (OTUs) within M2 was critical for module stability and heavy metal bioremediation. Additionally, members within M2 needed to form a positive relationship to cope with heavy metal contamination (As, Pb, Zn, Cu, and Cd). The study provides fundamental information for a deeper understanding of heavy metal bioremediation mechanisms in the Pb-Zn waste heap.

Comprehensive exploration of heavy metal contamination and risk assessment at two common smelter sites

This study investigated the horizontal, vertical and fractional distribution of heavy metals in the soil and the pollution and risk assessment of two smelter sites in Daye (a Cu smelter) and Zhuzhou (a Zn oxide smelter). Nine sampling points were reasonably established at each site, and nine soil samples were collected in each soil profile, with a total of 81 samples at each site. The results indicated that only As concentration was exceeded in most of the samples from the Daye site, and several were contaminated with multiple heavy metals, i.e. As, Cd and Pb; the values exceeding the standard were significant. Most of the samples at the Zhuzhou site were contaminated with many heavy metals, i.e. As, Cd, Pb and Ni. With increasing depth, the proportion of the acid-soluble and reducible heavy metal fraction decreased, while the proportion of the oxidized and residual fraction increased. The pollution index (PI) indicated that As at all positions, and Cd and Pb at several positions at the Daye site, as well as Cd and Pb at all points of Zhuzhou should have received more attention. The Nemerow integrated pollution index (NIPI) showed that a few sampling points in Daye were severely polluted, i.e. the points D5 with the value of 77.49 and the point D7 with 62.33, were more than the threshold value with 3 of severe pollution. Almost all sampling points in Zhuzhou were severely polluted, but the pollution degree was slightly lower than at Daye. The hazard index (HI) indicated the potential non-carcinogenic risk at the Daye and Zhuzhou sites. These values were unacceptable for both adults and children. The carcinogenic risk (CR) index indicated that the potential carcinogen risk due to As and Ni contamination were unacceptable at both sites, especially for children with 9.27E-03 and 1.99E-03 of As and Ni at Daye site, while 4.55E-03 and 4.09E-03 at Zhuzhou site. Strict control of industrial waste residues and smelters emissions into the soil is necessary to avoid further aggravation of heavy metal pollution.

Cd immobilization and soil quality under Fe-modified biochar in weakly alkaline soil

Cost-effective and environment-friendly implementation techniques are critical to the success of remediation in large-scale cadmium (Cd) contaminated agricultural soil. Field experiments were conducted to investigate the effect of Fe-modified biochar on Cd bioavailability in soils and uptake by maize (Zea mays L.), soil aggregate distribution and stability, and microbial community composition in weakly alkaline Cd-contaminated soil. Results showed that Fe-modified biochar optimized the structure and stability of soil aggregates. Moreover, the content of soil organic carbon increased by 6.59%-20.36% when compared with the control groups. However, DTPA-Cd concentration under the treatment of Fe-modified biochar was suffered by 37.74%-41.65% reduction in contrast with CK, and the significant decrease (P < 0.05) was obtained at 0.5% Fe-modified biochar. Moreover, sequential extraction procedures showed that the acid soluble and reducible states of Cd was converted into oxidizable and residual form. The addition of Fe-modified biochar inhibited Cd accumulation in maize, being 41.31%-76.64% (Zhengdan 958), 38.19%-70.95% (Liyu 86) and 52.30%-59.95% (Sanbei 218) reduction, respectively, in contrast with CK. The activity of catalase, urease and alkaline phosphatase in soil increased gradually with the addition of Fe-modified biochar. The enhancement in the number of soil bacterial OTUs and the values of Shannon, Chao1, ACE index indicated that Fe-modified biochar promoted the richness and diversity of bacterial communities. Therefore, the improvements of soil environment and biological quality indicated that Fe-modified biochar should be an alternative agent on remediation of Cd-contaminated soils.

Effects of Heavy Metals/Metalloids and Soil Properties on Microbial Communities in Farmland in the Vicinity of a Metals Smelter

Microorganisms play a fundamental role in biogeochemical cycling and are highly sensitive to environmental factors, including the physiochemical properties of the soils and the concentrations of heavy metals/metalloids. In this study, high-throughput sequencing of the 16S rRNA gene was used to study the microbial communities of farmland soils in farmland in the vicinity of a lead–zinc smelter. Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, and Gemmatimonadetes were the predominant phyla in the sites of interest. Sphingomonas, Gemmatimonas, Lysobacter, Flavisolibacter, and Chitinophaga were heavy metal-/metalloid-tolerant microbial groups with potential for bioremediation of the heavy metal/metalloid contaminated soils. However, the bacterial diversity was different for the different sites. The contents of heavy metal/metalloid species and the soil properties were studied to evaluate the effect on the soil bacterial communities. The Mantel test revealed that soil pH, total cadmium (T-Cd), and available arsenic played a vital role in determining the structure of the microbial communities. Further, we analyzed statistically the heavy metals/metalloids and the soil properties, and the results revealed that the microbial richness and diversity were regulated mainly by the soil properties, which correlated positively with organic matter and available nitrogen, while available phosphorus and available potassium were negatively correlated. The functional annotation of the prokaryotic taxa (FAPROTAX) method was used to predict the function of the microbial communities. Chemoheterotrophy and airborne chemoheterotrophy of the main microbial community functions were inhibited by soil pH and the heavy metals/metalloids, except in the case of available lead. Mantel tests revealed that T-Cd and available zinc were the dominant factors affecting the functions of the microbial communities. Overall, the research indicated that in contaminated soils, the presence of multiple heavy metals/metalloids, and the soil properties synergistically shaped the structure and function of the microbial communities.

APORTES Y DIFICULTADES DE LA METAGENÓMICA DE SUELOS Y SU IMPACTO EN LA AGRICULTURA

Los microorganismos son de gran interés porque colonizan todo tipo de ambiente, sin embargo, uno de los problemas al que nos enfrentamos para conocer su diversidad biológica es que no todos los microorganismos son cultivables. El desarrollo de nuevas tecnologías como la generación de vectores de clonación aunado al desarrollo de técnicas de secuenciación de alto rendimiento ha favorecido el surgimiento de una nueva herramienta llamada metagenómica, la cual nos permite estudiar genomas de comunidades enteras de microorganismos. Debido a que ningún ambiente es idéntico a otro, es importante mencionar que dependiendo del tipo de muestra a analizar será el tipo de reto al cual nos enfrentaremos al trabajar con metagenómica, en el caso específico del suelo existen diversas variantes como la contaminación del suelo con metales pesados o diversos compuestos químicos que podrían limitar los estudios. Sin embargo, pese a las limitaciones que el mismo ambiente presenta, la metagenómica ha permitido tanto el descubrimiento de nuevos genes como la caracterización de las comunidades microbianas que influyen positivamente en el desarrollo de plantas, lo cual en un futuro podría generar un gran impacto en la agricultura. En este artículo se realizó una revisión de diversas investigaciones que han empleado metagenómica, reportadas en las bases de datos de PudMed y Google Schoolar, con el objetivo de examinar los beneficios y limitaciones de las diversas metodologías empleadas en el tratamiento del ADN metagenómico de suelo y el impacto de la metagenómica en la agricultura.

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.

Apricot shell- and apple tree-derived biochar affect the fractionation and bioavailability of Zn and Cd as well as the microbial activity in smelter contaminated soil

The aim of this study was to elucidate the effects of apricot shell-derived biochar (ASB) and apple tree-derived biochar (ATB) on soil properties, plant growth, microbial communities, enzymatic activities, and Zn and Cd fractionation and phytoavailability in mining soils. Smelter soil contaminated by Zn (1860.0 mg kg^-1) and Cd (39.9 mg kg^-1) was collected from Fengxian, China, treated with different doses (0 (control), 1, 2.5, 5, and 10% w/w) of both biochars and cultivated by Brassica juncea in a greenhouse pot experiment. The acid-soluble, reducible, oxidizable, and residual fraction and plant tissue concentrations of Zn and Cd were determined. Biochar addition improved plant growth (22.6-29.4%), soil pH (up to 0.94 units), and soil organic matter (up to 4-fold) compared to the control. The ASB and ATB, particularly ATB, reduced the acid-soluble (21-26% for Zn and 15-35% for Cd) and the reducible (9-36% for Zn and 11-19% for Cd) fractions of Zn and Cd and altered these fractions in the organic and residual fractions. Therefore, the biochars decreased the metal concentrations in the roots (36-41% for Zn and 33-37% for Cd) and shoots (25-31% for Zn and 20-29% for Cd), which might be due to the increase in pH, biochar liming effects, and metal sorption by the biochar. The biochars impact on the bacterial community composition was selective. The ASB and ATB decreased the activities of soil β-glucosidase, dehydrogenase, and alkaline phosphatase while increasing the urease activity. The biochars, particularly ATB, can be considered as effective soil amendments for reducing the phytotoxicity of Zn and Cd in contaminated soils, improving plant growth, enhancing the abundance of specific bacterial groups and increasing urease activity; however, more attention should be paid to their negative effects on the activities of β-glucosidase, dehydrogenase, and alkaline phosphatase.

Effects of tree-herb co-planting on the bacterial community composition and the relationship between specific microorganisms and enzymatic activities in metal(loid)-contaminated soil

Tree-herb co-planting is regarded as an ecologically sustainable approach for the remediation of metal(loid)-contaminated soil. In this study, two herb species, Pteris vittata L. and Arundo donax L., and two woody species, Morus alba L. and Broussonetia papyrifera L., were selected for the tree-herb co-planting, and their impacts on the changing of microbial community structure in metal(loid)-contaminated soil were studied by high-throughput sequencing. The results showed that the microbial diversity was stably maintained by the tree-herb interactions, while the composition of the microbial community was clearly affected in metal(loid)-contaminated soil. According to the Venn and flower diagrams, heat map and principal coordinate analysis, both plant monocultures and co-planting had specific microbial community structures, which suggested that the composition and abundance of bacterial communities varied between plant monoculture and tree-herb co-planting treatments. In particular, A. donax L. played a vital role in increasing the abundances of Cyanobacteria (>1%) in metal(loid)-contaminated soil when co-planted with woody plants. Furthermore, some specific microorganisms combined with plants played a key role in improving enzyme activity in the contaminated soil. Correspondingly, sucrase and acid phosphatase activities in monoculture and co-planting treatments significantly (p < 0.05) increased by 1.05-3.37 and 7.24-20.3 times. These results indicated that the rhizospheric interactions in the tree-herb co-planting system positively affected the soil microbes and had stronger impacts on the composition of soil microorganisms, which was closely related to the improvement of the biological quality in the metal(loid)-contaminated soil.

Concentration and Community of Airborne Bacteria in Response to Cyclical Haze Events During the Fall and Midwinter in Beijing, China

Since 2013, severe haze events frequently have occurred in Beijing between October and March, which have created a significant public health threat. Although variations in the chemical composition of these haze events have been studied widely, information pertaining to airborne bacteria in such haze events remains limited. In this study, we characterized the concentration, community structure, and composition of the airborne bacteria in response to nine haze events that occurred between October 1, 2015, and January 5, 2016. We also analyzed the correlations of airborne bacteria (concentration, community structure, and composition) with pollution levels and meteorological factors. The results indicated that airborne bacterial concentration showed a positive cyclical correlation with the haze events, but the bacterial concentration plateaued at the yellow pollution level. In addition, we found particulate matter (PM₁₀) and relative humidity to be key factors that significantly affected the airborne bacterial concentration and community structure. Moreover, Halomonas and Shewanella were enriched on haze days for all nine of the haze events. Finally, the correlations between haze pollution and airborne bacteria in midwinter were weaker than those in fall and early winter, indicating an obvious staged distinction among the effects of haze on airborne bacteria. Our study illuminated the dynamic variation of bioaerosols corresponding to the cyclical haze events and revealed the interactions among air pollution, climate factors (mainly relative humidity), and airborne bacteria. These results imply that different strategies should be applied to deal with the potential threat of airborne bacteria during haze events in different seasons.

Improvement of biochar and bacterial powder addition on gaseous emission and bacterial community in pig manure compost

Effect of bamboo biochar (BC) combined with two bacterial powders (B) on gaseous emission and variety of bacterial community during pig manure (PM) composting was investigated. The results showed that treatments of BC, BC + B1 and BC + B2 can reduce peak gaseous emission by 54%, 80% and 69% for CH₄, respectively, while 37%, 45% and 45% for N₂O, respectively, and 13%, 19% and 26% for NH₃, respectively. The evolution of the bacterial community quantified with 16S rDNA analysis showed that in the thermophile stage, total relative abundance percentage of bacterial phyla of Firmicutes and Proteobacteria reached 97%, 97%, 93% and 96% for CK, BC, BC + B1 and BC + B2, respectively. Effects of BC on the compost bacterial community variation analysis proved bacterial activity in the thermophile stage was controlled by the content of dissolved organic carbon and temperature of the compost mixture, while electrical conductivity and total kjeldahl nitrogen also influenced compost maturity stage.