Heavy metal pollution decreases microbial abundance, diversity and activity within particle-size fractions of a paddy soil

Microbial communities in biosolids-amended soils: A critical review of high-throughput sequencing approaches

Sustainable reuse of treated wastewater sludge or biosolids in agricultural production requires comprehensive understanding of their risks and benefits. Microbes are central mediators of many biosolids-associated risks and benefits, however understanding of their responses to biosolids remains minimal. Application of biosolids to soils amounts to a coalescence of two distinct microbial communities adapted to vastly different matrices. High-throughput DNA and RNA sequencing (HTS) approaches are required to accurately describe the compositional and functional outcomes of this process as they currently provide the highest possible resolution to deal with complex community-scale phenomena. Furthermore, linkage of HTS data to physicochemical and functional data can reveal biotic and abiotic drivers of coalescence, impacts of biosolids-borne contaminants and the collective downstream implications for soil and plant health. Here we review the current body of literature examining microbial communities in biosolids-amended soils using HTS of total community DNA and RNA. We provide a critical synthesis of soil microbial community composition and functional responses, the physical, chemical and biological drivers of these responses, and the influence of three major biosolids-borne anthropogenic contaminants of concern; antimicrobials and antimicrobial resistance genes, plastics, and per- and polyfluoroalkyl substances (PFAS). Finally, we identify methodological limitations and outstanding research questions precluding a holistic understanding of microbial responses in biosolids-amended soils and envision future research whereby sequence-based microbial ecology is integrated with soil, plant, and contaminant data to preserve soil health, support plant productivity, and remediate contaminants.

Soil Microbial Responses to Varying Environmental Conditions in a Copper Belt Region of Africa: Phytoremediation Perspectives

The mining industry in the copper belt region of Africa was initiated in the early 1900s, with copper being the main ore extracted to date. The main objectives of the present study are (1) to characterize the microbial structure, abundance, and diversity in different ecological conditions in the cupriferous city of Lubumbashi and (2) to assess the metal phytoextraction potential of Leucaena leucocephala, a main plant species used in tailing. Four ecologically different sites were selected. They include a residential area (site 1), an agricultural dry field (site 2), and an agricultural wetland (site 3), all located within the vicinity of a copper/cobalt mining plant. A remediated tailing was also added as a highly stressed area (site 4). As expected, the highest levels of copper and cobalt among the sites studied were found at the remediated tailing, with 9447 mg/kg and 2228 mg/kg for copper and cobalt, respectively. The levels of these metals at the other sites were low, varying from 41 mg/kg to 579 mg/kg for copper and from 4 mg/kg to 110 mg/kg for cobalt. Interestingly, this study revealed that the Leucaena leucocephala grown on the remediated sites is a copper/cobalt excluder species as it accumulates soil bioavailable metals from the rhizosphere in its roots. Amplicon sequence analysis showed significant differences among the sites in bacterial and fungal composition and abundance. Site-specific genera were identified. Acidibacter was the most abundant bacterial genus in the residential and remediated tailing sites, with 11.1% and 4.4%, respectively. Bacillus was predominant in both dry (19.3%) and wet agricultural lands (4.8%). For fungi, Fusarium exhibited the highest proportion of the fungal genera at all the sites, with a relative abundance ranging from 15.6% to 20.3%. Shannon diversity entropy indices were high and similar, ranging from 8.3 to 9 for bacteria and 7.0 and 7.4 for fungi. Β diversity analysis confirmed the closeness of the four sites regardless of the environmental conditions. This lack of differences in the microbial community diversity and structures among the sites suggests microbial resilience and physiological adaptations.

Analysis of changes and influencing factors of stablization treatment effects and bioavailability after freeze-thaw: a case study of Pb-contaminated soil in a non-ferrous metal factory in Northeast China

Introduction

Solidification/Stabilization techniques are commonly used for the containment and isolation of Pb-contaminated soil, but they cannot reduce the amount of contaminants. Freeze - thaw after stabilization may affect Pb's environmental behavior and increase the uncertainty of environmental risk.

Methods

In vitro experiments can simulate the bioavailability of heavy metals to the human body, accurately assessing their environmental health risks. In this study, soil samples from Pbcontaminated site are collected from a non-ferrous metal plant in Northeastern China. Through the results of stabilization and freeze-thaw after stabilization experiments, analyzing the changes of physicochemical property, Pb treatment effects (total concentration, leaching concentration, and occurrence forms) and microbial communities, and studying the influencing factors of Pb's bioavailability.

Result and discussion

The results show that stabilization and freeze - thaw after stabilization directly alter soil physicochemical property, thereby affecting the leaching and occurrence form of Pb and microbial communities, and closely related to changes in bioavailability of Pb. Both stabilization and freeze-thaw treatment reduced the leaching concentration of Pb, decreased the proportion of available Pb (acid-soluble state, oxidation state and reduction state), increased the bioavailability of Pb in the gastric phase, but decreased in the intestinal phase; And the dominant bacterial phylum in the soil changed to Firmicutes, the dominant bacterial genus changed to Bacillus; The analysis of the results shows that the bioavailability of Pb is related to soil pH, cation exchange capacity (CEC), soil organic matter (SOM), soil moisture content (SMC), Pb (leaching, acid soluble state, oxidation state, residual state), types of microorganisms in soil.

Chromium contamination affects the fungal community and increases the complexity and stability of the network in long-term contaminated soils

Chromium (Cr) contamination can adversely affect soil ecology, yet our knowledge of how fungi respond to Cr contamination at heavily contaminated field sites remains relatively limited. This study employed high-throughput sequencing technology to analyze fungal community characteristics in soils with varying Cr concentrations. The results showed that Cr contamination significantly influenced soil fungi's relative abundance and structure. Mantel test analysis identified hexavalent chromium (Cr(VI)) as the primary factor affecting the structure of the soil fungal community. In addition, FUNGuild functional prediction analysis exhibited that Cr contamination reduced the relative abundance of Pathotroph and Symbiotroph trophic types. High concentrations of Cr may lead to a drop in the relative abundance of Animal Pathogens. Molecular ecological network analysis showed that Cr contamination increased interactions among soil fungi, thereby enhancing the stability and complexity of the network. Within these networks, specific keystone taxa, such as the genus Phanerochaete, exhibited properties capable of removing or reducing the toxicity of heavy metals. Our studies suggest that Cr contamination can alter indigenous fungal communities in soil systems, potentially impacting soil ecosystem function.

The increase of particle size shifts the biogeochemical cycle functions of mineral-associated microorganisms and weakens the mineral-associated organic carbon sink in mangrove soils

Mineral-organic matter-microbe interactions greatly impact the biogeochemical processes and biodiversity in soils. An increasing trend of particle size (PS) in mangrove soils has been observed because of the relative sea level rise. However, the impacts of PS increase on the microbial biogeochemical functions and carbon sink in the mineral-associated microcosms are exceedingly nebulous. This work showed a remarkable difference in the communities of mineral-associated microorganisms (MMOs) in various PS fractions. Heavy metal contents and urease activity were the factors that mostly driven the MMO community variation in different PS fractions. Large PS fraction attenuated the stability of MMO communities according to the co-occurrence network characteristics. The PS increase significantly (P < 0.05) lowered the gene abundances for carbon input (e.g., carbon fixation) and raised the gene abundances for carbon loss (e.g., aerobic respiration). Combined with the significant decrease of mineral-associated organic carbon (MOC) in large PS fraction (P < 0.05), this work inferred that the PS increase could weaken the MOC sink partially due to the MMO function shift for carbon cycle. The current work indicated unhealthy changes of MMO communities and MOC storage in mangrove soils, and PS was of significance as an indicator for predicting the carbon sink function, especially for the stable form, such as MOC, in the soils of mangroves under the ecological background of climate migration.

IMPORTANCE

Carbon with stable forms, such as mineral-associated organic carbon (MOC), is crucial for the sink capabilities in mangrove soils, and mineral-associated microorganisms (MMOs) are important players for the formation and metabolism of MOC. Therefore, the future successions of the MMO functions and MOC contents under the background of climate change are of value for a deeper understanding of mangrove ecology. The relative sea level rise caused by the global warming results in the increase of mangrove soil particle size (PS), which provides distinct microcosms for MMOs and MOC. However, the responses of MMO functions and MOC content to the PS increase of mangrove soils are unknown. The current study aims to reveal the succession regulations of MMO functions and their potential ecological impacts for the storages of MOC in different PS fractions, therefore widening our knowledge of future function migration and promoting the research development of mangrove.

Fungal community determines soil multifunctionality during vegetation restoration in metallic tailing reservoir

Microorganisms are pivotal in sustaining soil functions, yet the specific contributions of bacterial and fungal succession on the functions during vegetation restoration in metallic tailing reservoirs remains elusive. Here, we explored bacterial and fungal succession and their impacts on soil multifunctionality along a ∼50-year vegetation restoration chronosequence in China's largest vanadium titano-magnetite tailing reservoir. We found a significant increase in soil multifunctionality, an index comprising factors pertinent to soil fertility and microbially mediated nutrient cycling, along the chronosequence. Despite increasing heavy metal levels, both bacterial and fungal communities exhibited significant increase in richness and network complexity over time. However, fungi demonstrated a slower succession rate and more consistent composition than bacteria, indicating their relatively higher resilience to environmental changes. Soil multifunctionality was intimately linked to bacterial and fungal richness or complexity. Nevertheless, when scrutinizing both richness and complexity concurrently, the correlations disappeared for bacteria but remained robust for fungi. This persistence reveals the critical role of the fungal community resilience in sustaining soil multifunctionality, particularly through their stable interactions with powerful core taxa. Our findings highlight the importance of fungal succession in enhancing soil multifunctionality during vegetation restoration in metallic tailing reservoirs, and manipulating fungal community may expedite ecological recovery of areas polluted with heavy metals.

Stability and heavy metals accumulation of soil aggregates under different land uses in the southwest coastal Bangladesh

Agricultural soil contamination is increasing day-by-day and becoming a major problem over the globe. Trace elements accumulation in the bulk soil is frequently documented, however, there is no precise mechanism of their distribution in the different soil aggregates level. We collected twelve composite soil samples from banana fields, fallow land, rice cultivated with pond water (rice field-I), and rice cultivated with rain water (rice field-II). We separated soil samples into four different size of aggregates (4-2, 2-0.25, 0.25-0.053, <0.053-mm) and then, aggregate stability (MWD), soil organic carbon (SOC), and heavy metals content (Pb, Cd, Cr, As, Fe, Mn, Zn, Ni, Co, Cu) in the soil samples were measured with different techniques. Results showed that MWD was higher in the rice-based land use, which was significantly contributed by SOC (p < 0.001). The concentration of Pb, As, Cd, Fe, and Mn were increased, while Cu and Zn concentration were reduced with increasing aggregate size (p < 0.05). In contrast, aggregate size did not influence on Ni and Co accumulation (p > 0.05). Moreover, macroaggregate acted as an accumulator for Fe, Mn, and As, while all the aggregate fractions acted as accumulators for Cu and Zn. Our study indicated that MWD, SOC, aggregate size and composition, and metal species were the controlling factors of trace elements accumulation and distribution in the various sizes of soil aggregates.

Urbanization reduces the stability of soil microbial community by reshaping the diversity and network complexity

Rapid urbanization considerably alters soil environment, biodiversity, and stability of terrestrial ecosystems. Soil microbial community, a key component of global biodiversity, plays a pivotal role in ecosystem stability and is highly vulnerable to urbanization. However, effects of urbanization on the diversity, stability, and network structure of soil microbial community remain poorly understood. Herein, we investigated the diversity and stability of soil microbial communities, including bacteria, fungi, and protists, across three regions with different levels of urbanization-urban, suburb, and ecoregion-using high-throughput sequencing techniques. Our results revealed that urbanization led to a notable decrease in the alpha diversity of soil microbial community, causing a significant reduction in soil stability, as assessed by the average variation degree (AVD). The loss of stability was linked to the diminished alpha diversity of the soil fungal and protistan communities, along with weakened interactions among bacteria, fungi, and protists. Notably, the majority of keystone species identified through network analysis were classified as bacteria (Proteobacteria) and displayed a strong positive correlation with the environmental factors influencing AVD. This highlights that the variability of bacteria and the immutability of fungi and protists are important to sustain soil microbial stability. Furthermore, structural equation models indicated that protistan diversity primarily drove soil microbial stability across all regions studied. In the suburban and ecoregion areas, soil microbial stability was directly influenced by the soil properties, bacterial diversity, and keystone species, as well as indirectly affected by heavy metals. These results underscore how urbanization can reduce the stability of soil microbial community via declined diversity and network complexity, whereas the establishment of ecoregions maybe contribute to preserve the diversity and stability of soil microbial community.

Assessing the impact of heavy metals on bacterial diversity in coastal regions of Southeastern India

Globally, there is growing concern over the environmental contamination of coastal ecosystems caused by anthropogenic activities. Here,we performed a study to evaluate the degree of heavy metal contamination in 5 different sediment samples collected from five sites along the Southeastern coast of India. Additionally, the research aims to explore the potential ecological implications of heavy metal contamination on the bacterial diversity, a crucial factor in upholding a sustainable ecosystem. A total of  seven heavy metals, i.e., chromium (Cr), copper (Cu), nickel (Ni), lead (Pb), mercury (Hg), cadmium (Cd) and arsenic (As), were assessed and quantified using inductively coupled plasma mass spectrometry. Targeted amplicon sequencing revealed that phylum Proteobacteria (36.9%) was the most dominating followed by Halobacterota (25.5%), Actinobacteriota (15%), Firmicutes (6.7%), Bacteroidota (4.0%), Thermoplasmatota (2.3%), Acidobacteriota (2.0%), Chloroflexi (1.6%), Planctomycetota (1.2%) and Crenarchaeota (1.1%). According to the alpha diversity estimate, lesser bacterial diversity was observed in areas with high pollution levels. Moreover, the physicochemical parameters of the sediments were analyzed. The contamination levels of the sediments were evaluated using the geo-accumulation index (Igeo), contamination factor (CF) and pollution loading index (PLI) to ascertain the comprehensive toxicity status of the sediments. The Igeo values revealed sediment pollution with metals such as Hg and Cd. The sediments obtained from the sampling site PU-01 showed the highest concentration of Hg pollution. Considering the ecotoxicological aspect, the estimated risk index (RI) values indicated a range from low to significant ecological risk.

Resistance mechanisms of cereal plants and rhizosphere soil microbial communities to chromium stress

Agricultural soils contaminated with heavy metals poison crops and disturb the normal functioning of rhizosphere microbial communities. Different crops and rhizosphere microbial communities exhibit different heavy metal resistance mechanisms. Here, indoor pot studies were used to assess the mechanisms of grain and soil rhizosphere microbial communities on chromium (Cr) stress. Millet grain variety 'Jingu 21' (Setaria italica) and soil samples were collected prior to control (CK), 6 hours after (Cr_6h), and 6 days following (Cr_6d) Cr stress. Transcriptomic analysis, high-throughput sequencing and quantitative polymerase chain reaction (qPCR) were used for sample determination and data analysis. Cr stress inhibited the expression of genes related to cell division, and photosynthesis in grain plants while stimulating the expression of genes related to DNA replication and repair, in addition to plant defense systems resist Cr stress. In response to chromium stress, rhizosphere soil bacterial and fungal community compositions and diversity changed significantly (p < 0.05). Both bacterial and fungal co-occurrence networks primarily comprised positively correlated edges that would serve to increase community stability. However, bacterial community networks were larger than fungal community networks and were more tightly connected and less modular than fungal networks. The abundances of C/N functional genes exhibited increasing trends with increased Cr exposure. Overall, these results suggest that Cr stress primarily prevented cereal seedlings from completing photosynthesis, cell division, and proliferation while simultaneously triggering plant defense mechanisms to resist the toxic effects of Cr. Soil bacterial and fungal populations exhibited diverse response traits, community-assembly mechanisms, and increased expression of functional genes related to carbon and nitrogen cycling, all of which are likely related to microbial survival during Cr stress. This study provides new insights into resistance mechanisms, microbial community structures, and mechanisms of C/N functional genes responses in cereal plants to heavy metal contaminated agricultural soils. Portions of this text were previously published as part of a preprint (https://www.researchsquare.com/article/rs-2891904/v1).

Industrial hemp (Cannabis sativa L.) can utilize and remediate soil strongly contaminated with Cu, As, Cd, and Pb by phytoattenuation

Industrial hemp (Cannabis sativa L.) has great application potential in heavy metal-polluted soils owing to its safe non-food utilization. However, the fate of heavy metals in different varieties of hemp planted in strongly contaminated natural soils remains unknown. Here, we investigated the growth, heavy metal uptake, distribution, and transfer of nine hemp varieties in soils strongly contaminated with Cu, As, Cd, and Pb. Hemp variety and metal type were the main factors affecting the growth and heavy metal uptake in hemp. The nine hemp varieties grew well in the contaminated soils; however, differences existed among the varieties. The biomass of Z3 reached 5669.1 kg hm-1, whereas that of Yunma No. 1 was only 51.8 % of Z3. The plant height, stalk diameter, and stalk bark thickness of Z3 were greater than those of the other varieties, reaching 168 cm, 9.2 mm, and 0.56 mm, respectively. Permanova's analysis revealed that the total effects of Cu, As, Cd, and Pb on the growth of the nine hemp varieties reached 60 %, with leaf As having the greatest effect, reaching 16 %. , Even in strongly contaminated soils, the nine varieties showed poor Cu, As, Cd, and Pb uptake. Most of the Cu, As, Cd, and Pb were retained in the root, reaching 57.7-72.4, 47.6-64.7, 76.0-92.9, and 70.0-87.8 %, respectively. Overall, the Cu, As, Cd, and Pb uptake of Wanma No.1 was the highest among the nine varieties, whereas that of Guangxi Bama was the lowest. These results indicate that hemp is a viable alternative for phytoattenuation in soils contaminated with heavy metals because of its ability to tolerate and accumulate Cu, As, Cd, and Pb in its roots, and Guangxi Bama is superior to the other varieties considering the safe utilization of hemp products.

Heavy metals drive microbial community assembly process in farmland with long-term biosolids application

Biosolids are considered an alternative to chemical fertilizers due to their rich nutrients. However, long-term biosolids application can lead to heavy metals accumulation, which severely affects soil microbial community compositions. The factors influencing soil microbial community assembly were explored under a 16-year long-term experiment with biosolids applications. Our results indicated that biosolids application significantly increased fungal richness while not for bacterial and arbuscular mycorrhizal (AM) fungal richness. Besides, biosolids application significantly affected soil bacterial, fungal compositions and AM fungal community. Soil microorganisms were clustered into different modules with bacterial and AM fungal communities were affected by both organic matter and heavy metals, while fungal communities were affected by heavy metals (Cr, Ni, and As). The soil bacterial community assembly was dominated by stochastic processes while the fungal and AM fungal community assemblies were mainly driven by deterministic processes. Random forest analysis showed that heavy metals were identified as major drivers (Hg, Cu, Cd, and Zn for bacteria, Pb and Cr for fungi, and As and Ni for AM fungi) of the community assembly process. Overall, our study highlights the significant role of heavy metals in shaping microbial community dynamics and gives a guide for controlling biosolids application.

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.

Microbial-driven mechanisms for the effects of heavy metals on soil organic carbon storage: A global analysis

Heavy metal (HM) enrichment is closely related to soil organic carbon (SOC) pools in terrestrial ecosystems, which are deeply intertwined with soil microbial processes. However, the influence of HMs on SOC remains contentious in terms of magnitude and direction. A global analysis of 155 publications was conducted to integrate the synergistic responses of SOC and microorganisms to HM enrichment. A significant increase of 13.6 % in SOC content was observed in soils exposed to HMs. The response of SOC to HMs primarily depends on soil properties and habitat conditions, particularly the initial SOC content, mean annual precipitation (MAP), initial soil pH, and mean annual temperature (MAT). The presence of HMs resulted in significant decreases in the activities of key soil enzymes, including 31.9 % for soil dehydrogenase, 24.8 % for β-glucosidase, 35.8 % for invertase, and 24.3 % for cellulose. HMs also exerted inhibitory effects on microbial biomass carbon (MBC) (26.6 %), microbial respiration (MR) (19.7 %), and the bacterial Shannon index (3.13 %) but elevated the microbial metabolic quotient (qCO2) (20.6 %). The HM enrichment-induced changes in SOC exhibited positive correlations with the response of MBC (r = 0.70, p < 0.01) and qCO2 (r = 0.50, p < 0.01), while it was negatively associated with β-glucosidase activity (r = 0.72, p < 0.01) and MR (r = 0.39, p < 0.01). These findings suggest that the increase in SOC storage is mainly attributable to the inhibition of soil enzymes and microorganisms under HM enrichment. Overall, this meta-analysis highlights the habitat-dependent responses of SOC to HM enrichment and provides a comprehensive evaluation of soil carbon dynamics in an HM-rich environment.

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.

Responses of microbial communities in rhizocompartments of king grass to phytoremediation of cadmium-contaminated soil

King grass has been recognized as a potential phytoremediation plant species due to its high biomass and resistance to heavy metals (HMs). However, the possible impacts of cadmium (Cd) contamination on rhizocompartments' microbial activities in association with king grass have not been extensively explored. The utilization of 16S rRNA gene and ITS sequencing was carried out to examine alterations in the bacterial and fungal communities in the rhizosphere and rhizoplane of king grass in response to low and high Cd stress. Results demonstrated that both bacterial and fungal communities' diversity and richness were negatively impacted by Cd stress, regardless of its concentration. However, evenness did not exhibit any significant response to either of the concentrations. Additionally, nonmetric multidimensional scaling (NMDS) ordination demonstrated a significant difference (p < 0.001) in microbial communities under different treatments. The abundance of bacterial taxa such as Steroibacter, Nitrospira, Pseudoxanthomonas, Cellvirio, Phenylobacterium, Mycobacterium, Pirellula and Aquicella was adversely affected under Cd stress while Flavobacterium, Gemmata, Thiobacillus and Gemmatimonas showed no prominent response, indicating their resistance to Cd stress. Like that, certain fungal taxa for instance, Cladosporium, Cercophora, Acremonium, Mortierella, Aspergillus, Penicillium, Glomus and Sebacina were also highly reduced by low and high Cd stress. In contrast, Fusarium, Thanatephorus, Botrytis and Curvularia did not show any response to Cd stress. The identified taxa may have a crucial role in the growth of king grass under heavy metal contamination, making them promising candidates for developing bioinoculants to encourage plant performance and phytoremediation capability in HM-contaminated soils.

Oxidative stress-induced DNA damage and DNA repair mechanisms in mangrove bacteria exposed to climatic and heavy metal stressors

Bacteria thriving in the mangrove ecosystem are major drivers of elemental cycles. Climate change and environmental stressors (heavy metals) influence the performance of these microorganisms, thereby affecting the biogeochemical cycle. The present study reports the genotoxic effect of climatic and heavy metal stressors on mangrove bacteria and their adaptation strategies. Comparative analysis between two bacterial strains, Bacillus stercoris GST-03 and Pseudomonas balearica DST-02 isolated from the Bhitarkanika mangrove ecosystem, Odisha, India, showed cellular injuries in response to various stressors as evident by declined growth, elevated levels of reactive oxygen species (ROS) and resulted DNA damage. B. stercoris GST-03 showed more tolerance towards acidic pH, whereas P. balearica DST-02 showed higher tolerance towards UV exposure and heavy metals (Lead and Cadmium). The adaptation strategies of the strains revealed a significant role of GST in ROS scavenging activity and the involvement of Nucleotide excision repair or SOS response pathways. However, irreparable DNA damage was observed at pH 9 and 200 ppm Cd in B. stercoris GST-03, and at pH 4, 1000 ppm of Pb and 200 ppm of Cd in P. balearica DST-02. The current findings provide a broad overview of bacterial response and adaptability concerning future climate and environmental changes.

Cadmium reduced methane emissions by stimulating methane oxidation in paddy soils

Flooded rice paddy fields are a significant source of anthropogenic methane (CH4) emissions. Cadmium (Cd) is one of the most common and toxic contaminants in paddy soils. However, little is known about how the soil microbial communities associated with CH4 emissions respond to the increasing Cd-stress in paddies. In this study, we employed isotopically 13C-labelled CH4, high-throughput sequencing analysis, and gene quantification analysis to reveal the effect and mechanism of Cd on CH4 emissions in paddy soils. Results showed that 4.0 mg kg-1 Cd addition reduced CH4 emissions by 16-99% in the four tested paddy soils, and significantly promoted the transformation of 13CH4 to 13CO2. Quantitative polymerase chain reaction (qPCR) demonstrated that Cd addition increased the abundances of pmoA gene, the ratios of methanogens to methanotrophs (mcrA/pmoA) showed a positive correlation with CH4 emissions (R2 = 0.798, p < 0.01). Furthermore, the composition of the microbial community containing the pmoA gene was barely affected by Cd addition (p > 0.05). This observation was consistent with the findings of a pure incubation experiment where methanotrophs exhibited high tolerance to Cd. We argue that microbial feedback to Cd stress amplifies the contribution of methanotrophs to CH4 oxidation in rice fields through the complex interactions occurring among soil microbes. Our study highlights the overlooked association between Cd and CH4 dynamics, offering a better understanding of the role of rice paddies in global CH4 cycling.

Bioremoval of heavy metals from aqueous solution using dead biomass of indigenous fungi derived from fertilizer industry effluents: isotherm models evaluation and batch optimization

The present work investigated the utilization of dead biomass of the highly multi-heavy metals tolerant indigenous fungal strain NRCA8 isolated from the mycobiome of fertilizer industry effluents that containing multiple heavy metal ions at high levels to remove Pb2+, Ni2+, Zn2+, and Mn2+ as multiple solutes from multi-metals aqueous solutions for the first time. Based on morphotype, lipotype and genotype characteristics, NRCA8 was identified as Cladosporium sp. NRCA8. The optimal conditions for the bioremoval procedure in the batch system were pH 5.5 for maximum removal (91.30%, 43.25%, and 41.50%) of Pb2+, Zn2+ and Mn2+ but pH 6.0 supported the maximum bioremoval and uptake of Ni2+ (51.60% and 2.42 mg/g) by NRCA8 dead biomass from the multi-metals aqueous solution, respectively. The 30 min run time supported the highest removal efficiency and uptake capacity of all heavy metals under study. Moreover, the equilibrium between the sorbent NRCA8 fungal biomass and sorbates Ni2+, Pb2+ and Zn2+ was attained after increasing the dead biomass dose to 5.0 g/L. Dead NRCA8 biomass was described by scanning electron microscopy, energy-dispersive X-ray spectroscopy and Fourier transform infrared spectrometer before and after biosorption of Pb2+, Ni2+, Zn2+ and Mn2+ under multiple metals system. The Langmuir, Freundlich and Dubinin-Kaganer-Radushkevich isotherms were applied to characterize the adsorption equilibrium between Pb2+, Ni2+, Mn2+ and Zn2+ and the adsorbent NRCA8. By comparing the obtained coefficient of regression (R2) by Freundlich (0.997, 0.723, 0.999, and 0.917), Langmiur (0.974, 0.999, 0.974, and 0.911) and Dubinin-Radushkevich (0.9995, 0.756, 0.9996 and 0.900) isotherms values for Pb2+, Zn2+, Ni2+ and Mn2+ adsorption, respectively, it was found that the isotherms are proper in their own merits in characterization the possible of NRCA8 for removal of Pb2+, Zn2+, Ni2+ and Mn2+. DKR isotherm is the best for Pb2+ and Ni2+ (0.9995 and 0.9996) while Langmiur isotherm giving a good fit to the Zn2+ sorption (0.9990) as well as Freundlich isotherm giving a good fit to the Mn2+ sorption (0.9170). The efficiencies of Cladosporium sp. NRCA8 dead biomass for bioremoval of heavy metals from real wastewater under the optimized conditions were Pb2+, Ag+, Mn2+, Zn2+ and Al3+ ˃ Ni2+ ˃ Cr6+ ˃ Co2+ ˃ Fe3+ ˃ Cu2+ ˃ Cd2+. Dead NRCA8 biomass showed efficient ability to adsorb and reduce harmful components in the industrial effluents to a level acceptable for discharge into the environment.

How does metal soil pollution change the plant mycobiome?

Microorganisms play a key role in plant adaptation to the environment. The aim of this study was to evaluate the effect of toxic metals present in the soil on the biodiversity of plant-related, endophytic mycobiota. The mycobiome of plants and soil from a Zn-Pb heap and a metal-free ruderal area were compared via Illumina sequencing of the ITS1 rDNA. The biodiversity of plants and fungi inhabiting mine dump substrate was lower than that of the metal free site. In the endosphere of Arabidopsis arenosa from the mine dump the number of endophytic fungal taxa was comparable to that in the reference population, but the community structure significantly differed. Agaricomycetes was the most notably limited class of fungi. The results of plant mycobiota evaluation from the field study were verified in terms of the role of toxic metals in plant endophytic fungi community assembly in a reconstruction experiment. The results presented in this study indicate that metal toxicity affects the structure of the plant mycobiota not by changing the pool of microorganisms available in the soil from which the fungal symbionts are recruited but most likely by altering plant and fungi behaviour and the organisms' preferences towards associating in symbiotic relationships.

Unlocking the secrets of soil microbes: How decades-long contamination and heavy metals accumulation from sewage water and industrial effluents shape soil biological health

Heavy metals contamination is posing severe threat to the soil health and environmental sustainability. Application of industrial and sewage waste as irrigation and growing urbanization and agricultural industry is the main reason for heavy metals pollution. Therefore, the present study was planned to assess the influence of different irrigation sources such as industrial effluents, sewage wastewater, tube well water, and canal water on the soil physio-chemical, soil biological, and enzymatic characteristics. Results showed that sewage waste and industrial effluents affect the soil pH, organic matter, total organic carbon, and cation exchange capacity. The highest total nickel (383.71 mg kg-1), lead (312.46 mg kg-1), cadmium (147.75 mg kg-1), and chromium (163.64 mg kg-1) were recorded with industrial effluents application. Whereas, industrial effluent greatly reduced the soil microbial biomass carbon (SMB-C), soil microbial biomass nitrogen (SMB-N), soil microbial biomass phosphorus (SMB-P), and soil microbial biomass sulphur (SMB-S) in the winter season at sowing time. Industrial effluent and sewage waste inhibited the soil enzymes activities. For instance, the minimum activity of amidase, urease, alkaline-phosphatase, β-glucosidase, arylsulphatase and dehydrogenase activity was noted with HMs contamination. The higher levels of metals accumulation was observed in vegetables grown in soil contaminated with untreated waste water and industrial effluent in comparison to soil irrigated with canal and tube well water. The mean increase in soil microbial parameters and enzyme activities was also observed in response to the change in season from winter to spring due to increase in soil mean temperature. The SMB-C, SMB-N, SMB-P and SMB-S showed significant positive correlation with soil enzymes (amidase, urease, alkaline-phosphatase, β-glucosidase, arylsulphatase and dehydrogenase). The heavy metals accumulation in soil is toxic to microorganisms and inhibits enzyme functions critical for nutrient cycling and organic matter decomposition and can disrupt the delicate balance of soil ecosystem and may lead to long-term damage of soil biological health.

Effect of simulated root exudates on the distribution, bioavailability, and fractionation of potentially toxic elements (PTEs) in various particle size fractions of zinc smelting slag: Implication of direct revegetation

Direct revegetation is a promising strategy for phytostabilization of metal smelting slag sites. Slag comes into direct contact with root exudates when slag sites undergo direct revegetation. The slag particle size fractions are considered the key factor influencing the geochemical behaviour of potentially toxic elements (PTEs). However, the effects of root exudates on the geochemical behaviours of PTEs in various slag particle size fractions remain unclear. Here, the effects of simulated root exudates of perennial ryegrass (Lolium perenne) directly revegetated at a zinc smelting slag site on the distribution, bioavailability, and fractionation of PTEs (Cu, Pb, Zn, and Cd) in various slag particle size fractions were investigated. The results showed that PTEs mainly occurred in the <1 mm slag particles; the mass loads of PTEs in the <1 mm slag particles were higher than those in the >1 mm slag particles. The bioavailability of Cu, Zn, and Cd rather than Pb in the slag increased as the particle size decreased. There was a decrease in the <0.25 and 1-2 mm slag particles and an increase in the 0.25-0.5, 0.5-1, and >2 mm slag particles in the presence of root exudates. Root exudates enhanced the transformation of acid-soluble PTEs into other more stable fractions in various slag particle size fractions. Root exudates enhanced the aggregation of slag particles associated with the migration of PTEs, causing differences in the geochemical behaviour of PTEs in various slag particle size fractions. These findings are beneficial for understanding the geochemical behaviour of PTEs in metal smelting slags undergoing direct revegetation and provide an important basis for the guidance of environmental risk management of the revegetated metal smelting slag sites.

Chromium contamination accentuates changes in the microbiome and heavy metal resistome of a tropical agricultural soil

The impacts of hexavalent chromium (Cr) contamination on the microbiome, soil physicochemistry, and heavy metal resistome of a tropical agricultural soil were evaluated for 6 weeks in field-moist microcosms consisting of a Cr-inundated agricultural soil (SL9) and an untreated control (SL7). The physicochemistry of the two microcosms revealed a diminution in the total organic matter content and a significant dip in macronutrients phosphorus, potassium, and nitrogen concentration in the SL9 microcosm. Heavy metals analysis revealed the detection of seven heavy metals (Zn, Cu, Fe, Cd, Se, Pb, Cr) in the agricultural soil (SL7), whose concentrations drastically reduced in the SL9 microcosm. Illumina shotgun sequencing of the DNA extracted from the two microcosms showed the preponderance of the phyla, classes, genera, and species of Actinobacteria (33.11%), Actinobacteria_class (38.20%), Candidatus Saccharimonas (11.67%), and Candidatus Saccharimonas aalborgensis (19.70%) in SL7, and Proteobacteria (47.52%), Betaproteobacteria (22.88%), Staphylococcus (16.18%), Staphylococcus aureus (9.76%) in SL9, respectively. Functional annotation of the two metagenomes for heavy metal resistance genes revealed diverse heavy metal resistomes involved in the uptake, transport, efflux, and detoxification of various heavy metals. It also revealed the exclusive detection in SL9 metagenome of resistance genes for chromium (chrB, chrF, chrR, nfsA, yieF), cadmium (czcB/czrB, czcD), and iron (fbpB, yqjH, rcnA, fetB, bfrA, fecE) not annotated in SL7 metagenome. The findings from this study revealed that Cr contamination induces significant shifts in the soil microbiome and heavy metal resistome, alters the soil physicochemistry, and facilitates the loss of prominent members of the microbiome not adapted to Cr stress.

Assembly processes of bacterial and fungal communities in metal(loid)s smelter soil

There are few studies on concurrent bacterial and fungal community assembly processes that govern the metal(loid)s biogeochemical cycles at smelters. Here, a systematic investigation combined geochemical characterization, co-occurrence patterns, and assembly mechanisms of bacterial and fungal communities inhabiting soils around an abandoned arsenic smelter. Acidobacteriota, Actinobacteriota, Chloroflexi, and Pseudomonadota were dominant in bacterial communities, whereas Ascomycota and Basidiomycota dominated fungal communities. The random forest model indicated the bioavailable fractions of Fe (9.58%) were the main positive factor driving the beta diversity of bacterial communities, and the total N (8.09%) was the main negative factor for fungal communities. Microbe-contaminant interactions demonstrate the positive impact of the bioavailable fractions of certain metal(loid)s on bacteria (Comamonadaceae and Rhodocyclaceae) and fungi (Meruliaceae and Pleosporaceae). The fungal co-occurrence networks exhibited more connectivity and complexity than the bacterial networks. The keystone taxa were identified in bacterial (including Diplorickettsiaceae, norank_o_Candidatus_Woesebacteria, norank_o_norank_c_AT-s3-28, norank_o_norank_c_bacteriap25, and Phycisphaeraceae) and fungal (including Biatriosporaceae, Ganodermataceae, Peniophoraceae, Phaeosphaeriaceae, Polyporaceae, Teichosporaceae, Trichomeriaceae, Wrightoporiaceae, and Xylariaceae) communities. Meanwhile, community assembly analysis revealed that deterministic processes dominated the microbial community assemblies, which were highly impacted by pH, total N, and total and bioavailable metal(loid) content. This study provides helpful information to develop bioremediation strategies for the mitigation of metal(loid)s-polluted soils.

Soil organic carbon fractionation of spoiled and unspoiled soils under different land use and land cover systems

Alteration in land use and land cover is the key factor affecting the soil carbon fractions and its distribution. A study was carried out to estimate the carbon fractions in soils of agricultural, forest and pasture lands in two different areas separated on the basis of industrial activities (spoiled and unspoiled) to get an insight on the long-term soil carbon storage potential. The results showed that the mean values of the total organic carbon (TOC) and various fractions are significantly different between the land use types (p < 0.05). Irrespective of the land uses, the forest land showed significantly higher TOC (7.97) than agricultural land (6.98) and pasture lands (6.68). Further, evaluation of carbon management index (CMI) indicated that forest lands had highest CMI value compared to the other land uses. The spoiled area had significantly higher TOC and carbon fractions than their respective counterparts in the unspoiled area (p < 0.05) due to the negative industrial impact on soil biological processes. The PCA separates the sources of different carbon fractions and revealed an association of N (nitrogen) and K (potassium) with VL (very labile) and L (labile) fractions and the association of P (phosphorous) with stable R (recalcitrant) form. Therefore, it can be inferred from the present study that alterations in land use not only result in soil quality degradation but also trigger a reduction in potential for long term soil C sequestration.

Effects of cadmium and copper mixtures on antibiotic resistance genes in rhizosphere soil

The evolvement and development of antibiotic resistance in microorganisms may be influenced by metals; however, it is still unclear how cadmium (Cd) and copper (Cu) combined affect the distribution and presence of antibiotic-resistance genes (ARGs) in rhizosphere soil. The aims of this research were to (1) compare the distribution patterns of bacterial communities and ARGs in response to the effects of Cd and Cu both separately and combined; (2) explore the possible mechanisms underlying the variation in soil bacterial communities and ARGs in addition to the combined effects of Cd, Cu, and various environmental variables (nutrients, pH, etc.); and (3) provide a reference for assessing the risks of metals (Cd and Cu) and ARGs. The findings showed that the multidrug resistance genes acrA and acrB and the transposon gene intI-1 were present in high relative abundance in bacterial communities. Cadmium and Cu had a substantial interaction effect on the abundance of acrA, whereas Cu had a notable main effect on the abundance of intI-1. According to the network analysis, the strong links between bacterial taxa and specific ARGs revealed that most ARGs were hosted by Proteobacteria, Actinobacteria, and Bacteroidetes. According to structural equation modeling, Cd had a larger effect on ARGs than Cu. Compared to previous analyses of ARGs, bacterial community diversity had little effect on ARGs in this study. Overall, the results may have important consequences for determining the possible hazard of soil metals and extend the understanding of how Cd and Cu co-select ARGs in rhizosphere soils.

Diversity and interaction of bacterial and microeukaryotic communities in sediments planted with different submerged macrophytes: Responses to decabromodiphenyl ether

Although various persistent organic pollutants (POPs) can affect microbial communities and functions in aquatic ecosystems, little is known about how bacteria and microeukaryotes respond to the POPs in sediments planted with different submerged macrophytes. Here, a 60-day microcosm experiment was carried out to investigate the changes in the diversity and interaction of bacterial and microeukaryotic communities in sediments collected from Taihu lake, either with decabromodiphenyl ether (BDE-209) own or combined with two common submerged macrophyte species (Vallisneria natans and Hydrilla verticillate). The results showed that BDE-209 significantly decreased the bacterial α-diversity but increased the microeukaryotic one. In sediments planted with submerged macrophytes, the negative effect of BDE-209 on bacterial diversity was weakened, and its positive effect on microeukaryotic one was strengthened. Co-occurrence network analysis revealed that the negative relationship was dominant in bacterial and microeukaryotic communities, while the cooperative relationship between microbial species was increased in planted sediments. Among nine keystone species, one belonging to bacterial family Thermoanaerobaculaceae was enriched by BDE-209, and others were inhibited. Notably, such inhibition was weakened, and the stimulation was enhanced in planted sediments. Together, these observations indicate that the responses of bacteria and microeukaryotes to BDE-209 are different, and their communities under BDE-209 contamination are more stable in sediments planted with submerged macrophytes. Moreover, the effects of plant species on the microbial responses to BDE-209 need to be explored by more specific field studies in the future.

Multi-faceted CRISPR-Cas9 strategy to reduce plant based food loss and waste for sustainable bio-economy - A review

Currently, international development requires innovative solutions to address imminent challenges like climate change, unsustainable food system, food waste, energy crisis, and environmental degradation. All the same, addressing these concerns with conventional technologies is time-consuming, causes harmful environmental impacts, and is not cost-effective. Thus, biotechnological tools become imperative for enhancing food and energy resilience through eco-friendly bio-based products by valorisation of plant and food waste to meet the goals of circular bioeconomy in conjunction with Sustainable Developmental Goals (SDGs). Genome editing can be accomplished using a revolutionary DNA modification tool, CRISPR-Cas9, through its uncomplicated guided mechanism, with great efficiency in various organisms targeting different traits. This review's main objective is to examine how the CRISPR-Cas system, which has positive features, could improve the bioeconomy by reducing food loss and waste with all-inclusive food supply chain both at on-farm and off-farm level; utilising food loss and waste by genome edited microorganisms through food valorisation; efficient microbial conversion of low-cost substrates as biofuel; valorisation of agro-industrial wastes; mitigating greenhouse gas emissions through forestry plantation crops; and protecting the ecosystem and environment. Finally, the ethical implications and regulatory issues that are related to CRISPR-Cas edited products in the international markets have also been taken into consideration.

Interactions among microorganisms functionally active for electron transfer and pollutant degradation in natural environments

Compared to single microbial strains, complex interactions between microbial consortia composed of various microorganisms have been shown to be effective in expanding ecological functions and accomplishing biological processes. Electroactive microorganisms (EMs) and degradable microorganisms (DMs) play vital roles in bioenergy production and the degradation of organic pollutants hazardous to human health. These microorganisms can strongly interact with other microorganisms and promote metabolic cooperation, thus facilitating electricity production and pollutant degradation. In this review, we describe several specific types of EMs and DMs based on their ability to adapt to different environments, and summarize the mechanism of EMs in extracellular electron transfer. The effects of interactions between EMs and DMs are evaluated in terms of electricity production and degradation efficiency. The principle of the enhancement in microbial consortia is also introduced, such as improved biomass, changed degradation pathways, and biocatalytic potentials, which are directly or indirectly conducive to human health.

Soil particle size fractions affect arsenic (As) release and speciation: Insights into dissolved organic matter and functional genes

Soil particle size fractions (PSFs) are important for arsenic (As) partitioning, migration, and speciation transformation. However, information is lacking about the environmental fate of As and its distribution on different PSFs. In the present study, two types of soils from mining areas were divided into four PSFs, including coarse sand (2-0.25 mm), fine sand (0.25-0.05 mm), silt (0.05-0.002 mm), and clay (< 0.002 mm) fractions. The results showed that As was enriched in the coarse sand, which was primarily affected by the content of organic carbon (OC), followed by iron (Fe), aluminum (Al), and manganese (Mn) (hydr)oxides. The elevated total As (TAs), As(III), organic As, Fe(II), and dissolved organic carbon (DOC) concentrations were mainly originated from the clay fraction. The intensified humification degree of DOM and promoted bacterial metabolism related to As/iron bioreduction were also exhibited in the clay fractions. The dynamics of As fractions in soils indicated the potential formation of secondary minerals and re-adsorption of As in the PSFs. The highest abundances of arrA, arsC, arsM, and Geo genes were found in the clay fraction, implying that the clay fraction potentially released more As, including As(III) and organic As. Results from the correlation analysis showed that elevated DOC concentrations promoted the catabolic responses of iron-reducing microorganisms and triggered microbial As detoxification. Overall, this study provides valuable information and guidance for the remediation of As-contaminated soils.

Effect of metal pollution on the distribution and co-occurrence pattern of bacterial, archaeal and fungal communities throughout the soil profiles

Metal pollution has raised negative impact on microbes, but little is known about the distribution and co-occurrence pattern of bacterial, fungal and archaeal communities along the soil profiles at multiple metal contamination sites. Here, we characterized the variations of metal concentrations and microbial communities with soil depth along five deep bores at the Tanghe Sewage Reservoir, a typical metal contamination area on the North China Plain. Co, Cd, Mg, Se, and Li were identified as the major contaminants in this area, and the pollution load index was 1.88, 1.54 and 1.62 in the shallow layer (0-0.6 m), deep layer (>2.0 m) and middle layer (0.6-2.0 m), respectively. The diversities and compositions of bacterial, archaeal and fungal communities varied significantly along the soil profiles. Deterministic process played a crucial role in shaping the difference of microbial community compositions among different soil layers, in which metal levels contributed more than soil physiochemical parameters. Furthermore, the interspecific co-occurrence network was most complex in the middle layer, indicating that metal pollution could decrease microbial network complexity. Bacterial keystone species in the co-occurrence networks showed both positive and negative correlations with polluted metals, whereas most archaeal and fungal keystone species were negatively related to multiple metals. These findings increased our understanding of distribution patterns, co-occurrence networks and environmental drivers of microbial communities in metal pollution soils.

Certain patterns of zinc, copper, and lead redistribution across the structural fractions of Chernozems and Urbic Technosols

The purpose of this work was to study the patterns of Zn, Cu, and Pb distribution in soil aggregates of various size fractions. Materials were Calcic Chernozems and Urbic Technosol of the Rostov agglomeration. Soil samples were passed through sieves with different mesh sizes (dry sieving). For the study, particle size fractions of > 10, 7-5, 5-3, 2-1, and < 0.25 mm were sampled, where the total forms of Zn, Cu, and Pb were examined by means of the X-ray fluorescence method. In the Zn content in both Calcic Chernozems and Urbic Technosol peaks in < 0.25-mm particle size fractions, the concentration decreases as particle size grows. Calcic Chernozems display Cu concentrations in mid-size soil particles of 2-1 and 5-3 mm. In Urbic Technosols, the lowest Cu concentration is typically found in particle size fractions of > 10 mm. Pb in Calcic Chernozems is concentrated in mid-size soil aggregates of 2-1 and 5-3 mm. However, Urbic Technosols tend to accumulate silt-fraction lead (< 0.25 mm). A higher zinc concentration in silt-fraction aggregates found in Urbic Technosols in comparison to Calcic Chernozems highlights the anthropogenic origin of a considerable part of this element's soil pool. Excessively high lead content in UR (urbic) horizons leads to the structure degradation and, consequently, to a transformed overall trend of HM distribution across the soil profile in general.

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.

Effect of calcination temperatures on the performance of rectorite for cadmium immobilization in soil: Freeze-thaw, plant growth, and microbial diversity

The immobilization of cadmium (Cd(II)) in soil using calcined rectorite (REC) was investigated in this research. The results of immobilization show that a small amount of REC calcined at 700 °C (REC-700 °C) could effectively immobilize 90% of Cd(II) in soil, while the immobilization efficiency of REC only reached 42%. Moreover, the immobilization efficiency of REC calcined at 300 °C and 500 °C (REC-300 °C and REC-500 °C) were lower than REC. To investigate the mechanism, the materials before and after immobilization were fully analyzed by Fourier transform infrared spectroscopy (FT-IR), powdery X-ray diffraction analysis (XRD), and scanning electron microscopy (SEM). The results indicate that the structure of REC has been changed after calcination at different temperatures and Cd(II) was successfully immobilized on materials. Losing free water, structural water and OH groups respectively, the layer spacing of REC-300 °C and REC-500 °C was shrunk. However, the crystal structure of REC was destroyed after calcination at 700 °C, resulting in the generation of new phases. According to the XRD result, more cadmium hydroxide (Cd(OH)₂) were produced on REC-700 °C, indicating that more OH groups were formed during immobilization. Furthermore, Tessier test demonstrates that Cd(II) in soil changed from exchangeable state and water soluble state to carbonate bound state and iron manganese oxide bound state during immobilization. The result of microbial community indicates that REC-700 °C can restore the microbial composition of Cd(II)-contaminated soil. The effects of pH, freeze-thaw, REC dosage, and initial heavy metal concentration were also evaluated to provide a theoretical basis for the subsequent application of the material in the remediation of contaminated soil.

Bacterial and fungal diversities examined through high-throughput sequencing in response to lead contamination of tea garden soil

Several studies have indicated that the heavy-metal content in tea is increasing gradually. Researchers examining the soil of more than 100 tea gardens in China have observed that lead content was higher in some soils. The effect of lead contamination on soil microorganisms in tea gardens was studied to determine the effect of lead on the essential functions of microorganisms in a tea garden soil ecosystem. Previous studies on pot experiments adopted the method of adding a single instance of pollution, which failed to comprehensively simulate the characteristics of the slow accumulation of heavy metals in soil. This study designed with two pollution modes (multistage and single instance) determined the content of soil lead in different forms according to the European Community Bureau of Reference extraction procedure. The community structure, species diversity and functional abundance of soil bacteria and fungi were examined by high-throughput sequencing. We observed that the content of four forms of lead was higher in the multistage contamination mode than in the single instance contamination mode. The effects of lead contamination on bacteria differed significantly (p < 0.05), and the abundance and diversity of bacteria were higher in the multistage contamination mode than in the single instance contamination mode. The community structure of fungi was more affected by lead than was that of bacteria. The content of each lead form was the environmental factor most strongly affecting soil bacteria and fungi. The predicted main function of the bacterial community was amino acid transport and metabolism, and the trophic mode of the fungal community was mainly pathotroph-saprotroph. This study revealed changes in soil microorganisms caused by different forms of lead and contamination methods in tea garden soil and provide a theoretical basis for examining the effects of lead contamination on soil microorganisms.

Submerged zone and vegetation drive distribution of heavy metal fractions and microbial community structure: Insights into stormwater biofiltration system

Biofiltration system is a widely used stormwater treatment option that is effective in removing heavy metals. The concentration and distribution of heavy metal fractions in biofiltration filter media, as well as the microbiota composition affected by the design parameters, are relatively novel concepts that require further research. A laboratory-scale column study was conducted to investigate the microbial community and the fractionation of heavy metals (Pb, Cu, Cr, and Cd) extracted from filter media samples, subjected to the presence of vegetation, submerged zone (SZ), and major environmental parameters (pH, water content). Sequential extractions revealed that, compared to the three other fractions (exchangeable fraction, reducible fraction, and oxidizable fraction), the residual fraction was the most represented for each metal (41 - 82 %). As a result, vegetation was found to reduce pH value, and significantly decrease the concentration of the exchangeable fraction of Pb in the middle layer, and the oxidizable fraction of Pb, Cu, Cd, and Cr in the middle and bottom layers (p < 0.05). The formation of an anoxic environment by submerged zone settlements resulted in a significant decrease in the concentration of reducible fractions and a significant increase in the concentration of oxidizable fractions for four heavy metals (p < 0.05). In addition, the analysis of the microbiota showed that the diversity and richness of microorganisms increased in the presence of SZ and plants. The dominant phylum in biofiltration was Proteobacteria, followed by Firmicutes, Bacteroidetes, Acidobacteria, and Actinobacteria as major phyla. Heavy metal fractions could regulate the structure of microbial communities in biofiltration. The findings of this study would enrich our understanding of the improvement of multi-metal-contaminated runoff treatment and highlight the impact of design parameters and heavy metal fractionation on microbial community structure in the biofiltration system.

The Effect of Heavy Metals on Microbial Communities in Industrial Soil in the Area of Piekary Śląskie and Bukowno (Poland)

The aim of this study was to determine the activity and structure of microbial communities in soils contaminated with heavy metals (HMs). To achieve this goal, soil samples were taken from two contaminated sites (i.e., Piekary Śląskie and Bukowno) in Poland. A wide range of methods were applied, including: total and metal-tolerant culturable bacteria enumeration; microbial community structure analysis using the phospholipid fatty acid method (PLFA); denaturing gradient gel electrophoresis (PCR-DGGE); and metabolic activity using BIOLOG and EcoPlateTM. Our studies showed that HMs negatively affected microbial community structure and activity in polluted soils. Apart from the contamination with HMs, other soil parameters like soil pH and water also impacted microbial community structure and growth. Metal-tolerant bacterial strains were isolated, identified and tested for presence of genes encoding HM tolerance using the polymerase chain reaction (PCR) methodology. Contamination with HMs in the tested areas was found to lead to development of metallotolerant bacteria with multiple tolerances toward Zn, Ni, Cd and Cu. Different genes (e.g., czcA, cadA and nccA) encoding HM efflux pumps were detected within isolated bacteria. Culturable bacteria isolated belonged to Proteobacteria, Actinobacteria and Bacteroidetes genera. Among non-culturable bacteria in soil samples, a significant fraction of the total bacteria and phyla, such as Gemmatimonadetes and Acidobacteria, were found to be present in all studied soils. In addition, bacteria of the Chloroflexi genus was present in soil samples from Piekary Śląskie, while bacteria of the Firmicutes genus were found in soil samples from Bukowno.

Effects of soil aging conditions on distributions of cadmium distribution and phosphatase activity in different soil aggregates

Aging behaviors of metals in the field differ from those in a controlled laboratory environment. Whether aging conditions influence the fates of metals in soil remains unclear. In this study, distributions of cadmium (Cd) and phosphatase activity were compared in soil aggregates (i.e., >2, 1-2, 0.25-1, and <0.25 mm) along a profile (0-5, 5-10, and 10-15 cm) at the end of 500-day aging experiments under both controlled laboratory and field conditions. Cd concentration in the 0-5 cm layer was lower and Cd concentration in the 5-10 cm layer was higher in field-aged soil compared to laboratory-aged soil. 25.26-35.62% of soil Cd was loaded in >2 mm aggregates of field-aged soils, and 58.41-66.95% was in laboratory-aged soils. Higher loadings of Cd in 0.25-1 and <0.25 mm aggregates were found in field-aged soil. A higher proportion of exchangeable Cd fraction (20.93% of total soil Cd) was found in the 0-5 cm layer of field-aged soil than in laboratory-aged soil (17.63%), while the opposite tendency was found in deeper soil layers. Soil phosphatase activities in field-aged soils were 1.13-1.26 times higher than in laboratory-aged soils. Phosphatase loadings in the >2 mm aggregates were lower and loadings in both the 1-2 and 0.25-1 mm aggregates were higher in field-aged soils than in laboratory-aged soils. Furthermore, correlation analysis and principal component analysis indicated that available Cd fractions accounted for most of the variations in phosphatase activities. In summary, the fates of the exogenous metal Cd differed between field and controlled laboratory conditions. To better understand the behaviors of heavy metals in soil, especially in a seasonal freeze-thaw area, further field studies are needed.

Long-term nickel contamination increased soil fungal diversity and altered fungal community structure and co-occurrence patterns in agricultural soils

Nickel (Ni) contamination imposes deleterious effects on the stability of soil ecosystem. Soil fungal community as a crucial moderator of soil remediation and biochemical processes has attracted more and more research interests. In the present study, soil fungal community composition and diversity under long-term Ni contamination were investigated and fungal interaction networks were built to reveal fungal co-occurrence patterns. The results showed that moderate Ni contamination significantly increased fungal diversity and altered fungal community structure. Functional predictions based on FUNGuild suggested that the relative abundance of arbuscular mycorrhizal fungi (AMF) significantly increased at moderate Ni contamination level. Ni contamination strengthened fungal interactions. Keystone taxa at different Ni contamination levels, such as Penicillium at light contamination, were identified, which might have ecological significance in maintaining the stability of fungal community to Ni stress. The present study provided a deeper insight into the effect of long-term Ni contamination on fungal community composition and co-occurrence patterns, and was helpful to further explore ecological risk of Ni contamination in cultivated field.

Microbial responses are unreliable indicators of copper ecotoxicity in soils contaminated by mining activities

Metal contamination of soil has become a serious environmental problem worldwide. Many studies have attempted to infer metal ecotoxicity from soil microbial responses. However, much of the data from these studies tends to be inconsistent and difficult to interpret. We hypothesized that microbial response would be a useful indicator of metal toxicity in soils contaminated by copper mining in Chile. Eighty-four topsoils (0-20 cm) were collected from three areas historically contaminated by copper mining (total Cu: 46-1106 mg kg^-1, soluble Cu: 0.05-2.3 mg kg^-1, pCu²⁺: 6.3-10, pH: 5.1-7.8, organic matter: 1.1-10%, clay: 0-28%). Based on soil metal concentrations and ecotoxicity thresholds, Cu was expected to be toxic to microorganisms in the studied soils, while the effects of other metals (total Zn: 79-672, As: 1.9-60, Pb: 19-220, Cd: 0.4-5.1 mg kg^-1) were expected to be minor. Soil microbial responses (microbial biomass and numbers, nitrogen mineralization and nitrification, and community-level physiological profiles) were also measured. The results showed that the different responses of soil microbes were not correlated with each other. Furthermore, the soil microbial responses were mainly influenced by the physicochemical properties of the soil, not by the metal concentrations in the soil. The effect of copper on the microbial response was either stimulating (positive) or toxic (negative). Of the soil microbial responses measured in this study, only the microbial biomass was useful for calculating dose-response curves. However, the microbial biomass response was not consistent among the different soil copper pools (total copper, soluble copper, and activity of free Cu²⁺ ions). It is important to emphasize that the thresholds obtained for copper toxicity cannot be adopted in a robust manner because of the different microbial responses in different sampling areas. Thus, in the copper-contaminated soils under study, microbial response was found to be an unreliable indicator of metal toxicity.

Chloride application weakens cadmium immobilization by lime in paddy rice soil

Contamination of agricultural products by cadmium (Cd) is a global health problem, causing chronic abnormalities. The consumption of rice, the most-consumed foods, is an important exposure route of Cd to human body. Chloride (Cl^-) is reported to increase Cd uptake by rice; however, the effect on Cd uptake and accumulation by rice in the presence of lime is not clear. Therefore, a pot culture experiment was performed to explore the influence of Cl^- on the absorption and accumulation of Cd in rice plants under lime remediation and its possible mechanisms. The results showed that Cl^- promoted Cd accumulation in rice grains, mainly because of increased Cd bioavailability in the soil and by impeding the formation of iron plaques on rice roots, which reduced chelating and precipitation of Cd. Moreover, increased overexpression of the main transporters of Cd in rice roots, including OsNramp5, OsNramp1, OsIRTs and OsHMA2, favored the upward translocation of Cd from the root to shoot and increased the transfer factors (TFs) from soil to root, root-stem, leaf to grain, and soil to grain. Therefore, the application of Cl-rich materials to Cd-contaminated rice fields should be avoided during liming of the soil for Cd immobilization.

Application of dry olive residue-based biochar in combination with arbuscular mycorrhizal fungi enhances the microbial status of metal contaminated soils

Biochar made-up of dry olive residue (DOR), a biomass resulting from the olive oil extraction industry, has been proposed to be used as a reclamation agent for the recovery of metal contaminated soils. The aim of the present study was to investigate whether the soil application of DOR-based biochar alone or in combination with arbuscular mycorrhizal fungi (AMF) leads to an enhancement in the functionality and abundance of microbial communities inhabiting metal contaminated soils. To study that, a greenhouse microcosm experiment was carried out, where the effect of the factors (i) soil application of DOR-based biochar, (ii) biochar pyrolysis temperature (considering the variants 350 and 500 °C), (iii) soil application dose of biochar (2 and 5%), (iv) soil contamination level (slightly, moderately and highly polluted), (v) soil treatment time (30, 60 and 90 days) and (vi) soil inoculation with Funneliformis mosseae (AM fungus) on β-glucosidase and dehydrogenase activities, FA (fatty acid)-based abundance of soil microbial communities, soil glomalin content and AMF root colonization rates of the wheat plants growing in each microcosm were evaluated. Biochar soil amendment did not stimulate enzyme activities but increased microbial abundances. Dehydrogenase activity and microbial abundances were found to be higher in less contaminated soils and at shorter treatment times. Biochar pyrolysis temperature and application dose differently affected enzyme activities, but while the first factor did not have a significant effect on glucosidase and dehydrogenase, a higher biochar dose resulted in boosted microbial abundances. Soil inoculation with F. mosseae favored the proliferation of soil AMF community and increased soil glomalin content as well as rates of AMF root colonization. This factor also interacted with many of the others evaluated to significantly affect soil enzyme activities, microbial abundances and AMF community. Our results indicate that the application of DOR-based biochar along with AMF fungi is an appropriate approach to improve the status of microbial communities in soils with a moderate metal contamination at short-term.

Recycled concrete aggregates are an economic form of urban riparian erosion management with limited impacts on freshwater chemistry and microbial diversity

Urban streams are at high risk of riparian erosion which impacts adjacent infrastructure stability. Methods to prevent stream erosion have been proposed including using recycled concrete (RC) materials to help stabilize the streambed; however, little is known about the environmental and biological impacts of using RC in urban streams. RC, new concrete (NC), and river rock controls were evaluated for their impact on water chemistry, water quality, and microbial community composition over 6.5 months in controlled laboratory mesocosms. Concentrations of 19 metals, nutrients, and pH of mesocosms containing RC were not significantly different from the river rock mesocosm throughout the experiment; however, NC mesocosms contained significantly higher (p < 0.05) concentrations of Co, As, Al, and V in mesocosm water samples compared to both RC and the river rock control. Microbial community diversity was not significantly impacted by mesocosm treatment. Microbial sequences mapping to taxa including Rhodoferax, Acidovorax, Nitrosomonas, and Novosphingobium were significantly more abundant (p < 0.01) in RC and NC mesocosm samples; however, the overall microbial community structure was similar across treatment types. Results from this study suggest that RC does not significantly alter the stream environment including microbial community diversity and is a viable option for use in stream restoration projects.

Long-term metal pollution shifts microbial functional profiles of nitrification and denitrification in agricultural soils

The increasing contamination of heavy metals in agricultural soils and its impact on the nitrogen (N) cycle and N use efficiency have attracted considerable attention in recent years. In this study, agricultural soils neighboring the Dabaoshan copper mining area (DBS) and Qingyuan electronic-waste recycling area (QY), in Guangdong, China, were sampled to study the interaction between heavy metals and nitrification/denitrification processes, especially the related microbial functional profiles. Results showed that the contamination of heavy metals affected nitrifiers and denitrifiers differently. The potential nitrification activity was about four times lower in metal-polluted soils compared with the unpolluted ones, with a significant decrease in the abundance of amoA and nxrB (p < 0.05) in the polluted samples. On the other hand, the potential denitrification activity was more metal-resistant, which attributed to its complex species composition as shown by a slightly higher α-diversity index, and was slightly higher (p > 0.05) in the polluted samples. Among the five denitrifying genes tested, nosZ gene had the highest increase and the nirK gene the most decrease in numbers and in the polluted soils. The metal-polluted soils had fewer correlations among N functional genes based on the co-occurrence network analysis. In addition, the core taxa of the whole bacterial community changed from copiotrophic to oligotrophic bacteria in the presence of heavy metals. Mantel test indicated that heavy metals were the dominant factors determining N-related genes while the bacterial community composition was due to a combination of heavy metal presence and soil properties such as TOC, NO₂^-, and pH. It is concluded that long-term heavy metals pollution potentially affected nitrifiers and denitrifiers differently as indicated by the shift in N functional genes and the change in nitrification/denitrification processes.

Latent Benefits and Toxicity Risks Transmission Chain of High Dietary Copper along the Livestock-Environment-Plant-Human Health Axis and Microbial Homeostasis: A Review

The extensive use of high-concentration copper (Cu) in feed additives, fertilizers, pesticides, and nanoparticles (NPs) inevitably causes significant pollution in the ecological environment. This type of chain pollution begins with animal husbandry: first, Cu accumulation in animals poisons them; second, high Cu enters the soil and water sources with the feces and urine to cause toxicity, which may further lead to crop and plant pollution; third, this process ultimately endangers human health through consumption of livestock products, aquatic foods, plants, and even drinking water. High Cu potentially alters the antibiotic resistance of soil and water sources and further aggravates human disease risks. Thus, it is necessary to formulate reasonable Cu emission regulations because the benefits of Cu for livestock and plants cannot be ignored. The present review evaluates the potential hazards and benefits of high Cu in livestock, the environment, the plant industry, and human health. We also discuss aspects related to bacterial and fungal resistance and homeostasis and perspectives on the application of Cu-NPs and microbial high-Cu removal technology to reduce the spread of toxicity risks to humans.

Effects of heavy metals on microorganisms and enzymes in soils of lead-zinc tailing ponds

Taking the soil around the lead-zinc tailings pound in the upper reaches of the Hanjiang River in Shaanxi Province as the research object, with tailings pond as the center, seven different belt zones were divided outwards, the contents of Pb, Cu, Zn, V, Ni, Cd in soil were analyzed, as well as soil basic respiration (SBR), microbial biomass carbon (MBC), microbial metabolic quotient (MMQ), and the activities of catalase, urease, cellulase, invertase and neutral phosphatase were also determined. The purpose was to reveal the intrinsic relationship between soil microbial, enzyme activities and heavy metal pollution, and to establish the characterization system of enzyme activities, soil heavy metal pollution degree, as well as microbial parameters. The results showed that: (1) The potential ecological risk index of six heavy metals was ranked as Cd > Cu > Pb > Ni > Zn > V. Cd was a high potential ecological risk, Cu was a medium potential ecological risk, and Zn, Pb, V and Ni were low potential ecological risk. The comprehensive evaluation result of Hakanson's potential ecological hazard index showed that, Zone I was of high potential risk level, Zone II, III and IV were of medium risk level, and Zone V, VI and VII were of low level. (2) Microbial biomass carbon (MBC) had a significant negative correlation or extremely significant negative correlation with 6 heavy metals, and microbial metabolic quotient (MMQ) had a significant positive correlation or extremely significant positive correlation with 6 heavy metals. MBC and MMQ were effective microbiological indexes to measure the quality status of soil, while SBR was not. (3) Catalase, cellulase, sucrase and neutral phosphatase activity had significant negative correlation with the contents of 6 heavy metals, and they could replicate the pollution degree of substantial metals in the soil. However, urease had no significant correlation with the contents of 6 heavy metals, which could not reflect the pollution degree of soil heavy metals.

Accumulation and relationship of metals in different soil aggregate fractions along soil profiles

Different aggregates vary in their ability to retain or adsorb metals in soil. Five soil profiles were sampled from different soil horizons and grouped, and the concentrations of Al, Mg, Ca, Fe, Mn, Cd, Cu and Pb were determined in six sizes of aggregates (> 2, 2-1, 1-0.6, 0.6-0.25, 0.25-0.053, < 0.053 mm). Significantly high (p < 0.05) structural stability indexes (SSI) and aggregate stability indexes (ASI) were recorded in the topsoil horizon, which may be attributed to the high soil organic matter (SOM) content in aggregates from topsoil. In addition, ASI and SSI were positively correlated (r = 0.569, p < 0.05) with each other, which indicated that the stability of soil aggregates could contribute to the structural stability of bulk soil. Moreover, accumulation factors (AF), principal component analysis (PCA) and Pearson's correlation coefficients were used for metal element assessment. The results indicated that SOM was not a key factor affecting the accumulation of Ca, Mg, Al, Fe, Mn, Pb, Cd and Cu in soil aggregates. In general, AF values for metal elements in microaggregates (< 0.25 mm) were high, which showed that metals preferred to accumulate in fine soil aggregates. The PCA and Pearson's correlation coefficients indicated that soil parent materials primarily controlled the distribution of Al, Ca, Fe, Mg and Mn, while materials derived from technogenic sources have important impacts on the distribution of Cd, Cu and Pb in soil aggregates along the soil profile.

Microbial Functional Diversity Correlates with Species Diversity along a Temperature Gradient

Microbial community diversity is often correlated with physical environmental stresses like acidity, salinity, and temperature. For example, species diversity usually declines with increasing temperature above 20°C. However, few studies have examined whether the genetic functional diversity of community metagenomes varies in a similar way as species diversity along stress gradients. Here, we investigated bacterial communities in thermal spring sediments ranging from 21 to 88°C, representing communities of 330 to 3,800 bacterial and archaeal species based on 16S rRNA gene amplicon analysis. Metagenomes were sequenced, and Pfam abundances were used as a proxy for metagenomic functional diversity. Significant decreases in both species diversity and Pfam diversity were observed with increasing temperatures. The relationship between Pfam diversity and species diversity followed a power function with the steepest slopes in the high-temperature, low-diversity region of the gradient. Species additions to simple thermophilic communities added many new Pfams, while species additions to complex mesophilic communities added relatively fewer new Pfams, indicating that species diversity does not approach saturation as rapidly as Pfam diversity does. Many Pfams appeared to have distinct temperature ceilings of 60 to 80°C. This study suggests that temperature stress limits both taxonomic and functional diversity of microbial communities, but in a quantitatively different manner. Lower functional diversity at higher temperatures is probably due to two factors, including (i) the absence of many enzymes not adapted to thermophilic conditions, and (ii) the fact that high-temperature communities are comprised of fewer species with smaller average genomes and, therefore, contain fewer rare functions. IMPORTANCE Only recently have microbial ecologists begun to assess quantitatively how microbial species diversity correlates with environmental factors like pH, temperature, and salinity. However, still, very few studies have examined how the number of distinct biochemical functions of microbial communities, termed functional diversity, varies with the same environmental factors. Our study examined 18 microbial communities sampled across a wide temperature gradient and found that increasing temperature reduced both species and functional diversity, but in different ways. Initially, functional diversity increased sharply with increasing species diversity but eventually plateaued, following a power function. This pattern has been previously predicted in theoretical models, but our study validates this predicted power function with field metagenomic data. This study also presents a unique overview of the distribution of metabolic functions along a temperature gradient, demonstrating that many functions have temperature "ceilings" above which they are no longer found.