Different responses of bacteria and fungi to environmental variables and corresponding community assembly in Sb-contaminated soil

Sb/As immobilization and soil function improvement under the combined remediation strategy of modified biochar and Sb-oxidizing bacteria at a smelting site

Antimony (Sb) and arsenic (As) lead to soil pollution and structural degradation at Sb smelting sites. However, most sites focus solely on Sb/As immobilization, neglecting the restoration of soil functionality. Here, we investigated the effectiveness of Fe/H2O2 modified biochar (Fe@H2O2-BC) and Sb-oxidizing bacteria (Bacillus sp. S3) in immobilizing Sb/As and enhancing soil functional resilience at an Sb smelting site. Over a twelve-month period, the leaching toxicity of As and Sb was reduced to 0.05 and 0.005 mg L-1 (GB3838-2002) respectively, with 1% (w/w) Fe@H2O2-BC and 2% (v/v) Bacillus sp. S3 solution. Compared to CK, the combination of Fe@H2O2-BC and Bacillus sp. S3 significantly reduced the bioavailable As/Sb by 98.00%/93.52%, whilst increasing residual As and reducible Sb fractions by 210.31% and 96.51%, respectively. The combined application generally improved soil aggregate structure, pore characteristics, and water-holding capacity. Fe@H2O2-BC served as a pH buffer and long-term reservoir of organic carbon, changing the availability of carbon substrates to bacteria. The inoculation of Bacillus sp. S3 facilitated the transformation of Sb(III)/As(III) to Sb(V)/As(V) and differentiated the composition and functional roles of bacterial communities in soils. The combination increased the abundance of soil saprotrophs by 164.20%, whilst improving the relative abundance of N- and S-cycling bacteria according to FUNGuild and FAPROTAX analysis. These results revealed that the integrated application was instrumental in As/Sb detoxification/immobilization and soil function restoration, which demonstrating a promising microbially-driven ecological restoration strategy at Sb smelting sites.

Bacterial-fungal interactions and response to heavy metal contamination of soil in agricultural areas

Introduction

Long-term heavy metal contamination of soil affects the structure and function of microbial communities. The aim of our study was to investigate the effect of soil heavy metal contamination on microorganisms and the impact of different heavy metal pollution levels on the microbial interactions.

Methods

We collected soil samples and determined soil properties. Microbial diversity was analyzed in two groups of samples using high-throughput sequencing technology. Additionally, we constructed microbial networks to analyze microbial interactions.

Results

The pollution load index (PLI) < 1 indicates that the area is not polluted. 1 < PLI < 2 represents moderate pollution. PLI was 1.05 and 0.14 for the heavy metal contaminated area and the uncontaminated area, respectively. Cd, Hg, Pb, Zn, and Cu were identified as the major contaminants in the contaminated area, with the contamination factors were 30.35, 11.26, 5.46, 5.19, and 2.46, respectively. The diversities and compositions of the bacterial community varied significantly between the two groups. Compared to the uncontaminated area, the co-occurrence network between bacterial and fungal species in the contaminated area was more complex. The keystone taxa of the co-occurrence network in the contaminated area were more than those in the uncontaminated area and were completely different from it.

Discussion

Heavy metal concentrations played a crucial role in shaping the difference in microbial community compositions. Microorganisms adapt to long-term and moderate levels of heavy metal contamination through enhanced interactions. Bacteria resistant to heavy metal concentrations may play an important role in soils contaminated with moderate levels of heavy metals over long periods of time.

Bacterial and fungal community structures in Hulun Lake are regulated by both stochastic processes and environmental factors

Microorganisms are a crucial component of lake ecosystems and significant contributors to biogeochemical cycles. However, the understanding of how primary microorganism groups (e.g., bacteria and fungi) are distributed and constructed within different lake habitats is lacking. We investigated the bacterial and fungal communities of Hulun Lake using high-throughput sequencing techniques targeting 16S rRNA and Internal Transcribed Spacer 2 genes, including a range of ecological and statistical methodologies. Our findings reveal that environmental factors have high spatial and temporal variability. The composition and community structures vary significantly depending on differences in habitats. Variance partitioning analysis showed that environmental and geographical factors accounted for <20% of the community variation. Canonical correlation analysis showed that among the environmental factors, temperature, pH, and dissolved oxygen had strong control over microbial communities. However, the microbial communities (bacterial and fungal) were primarily controlled by the dispersal limitations of stochastic processes. This study offers fresh perspectives regarding the maintenance mechanism of bacterial and fungal biodiversity in lake ecosystems, especially regarding the responses of microbial communities under identical environmental stress.IMPORTANCELake ecosystems are an important part of the freshwater ecosystem. Lake microorganisms play an important role in material circulation and energy flow owing to their unique enzymatic and metabolic capacity. In this study, we observed that bacterial and fungal communities varied widely in the water and sediments of Hulun Lake. The primary factor affecting their formation was identified as dispersal limitation during stochastic processes. Environmental and geographical factors accounted for <20% of the variation in bacterial and fungal communities, with pH, temperature, and dissolved oxygen being important environmental factors. Our findings provide new insights into the responses of bacteria and fungi to the environment, shed light on the ecological processes of community building, and deepen our understanding of lake ecosystems. The results of this study provide a reference for lake management and conservation, particularly with respect to monitoring and understanding microbial communities in response to environmental changes.

Toxic metal contamination effects mediated by hotspot intensity of soil enzymes and microbial community structure

Metal contamination from mine waste is a widespread threat to soil health. Understanding of the effects of toxic metals from mine waste on the spatial patterning of rhizosphere enzymes and the rhizosphere microbiome remains elusive. Using zymography and high-throughput sequencing, we conducted a mesocosm experiment with mine-contaminated soil, to compare the effects of different concentrations of toxic metals on exoenzyme kinetics, microbial communities, and maize growth. The negative effects of toxic metals exerted their effects largely on enzymatic hotspots in the rhizosphere zone, affecting both resistance and the area of hotspots. This study thus revealed the key importance of such hotspots in overall changes in soil enzymatic activity under metal toxicity. Statistical and functional guild analysis suggested that these enzymatic changes and associated microbial community changes were involved in the inhibition of maize growth. Keystone species of bacteria displayed negative correlations with toxic metals and positive correlations with the activity of enzymatic hotspots, suggesting a potential role. This study contributes to an emerging paradigm, that changes both in the activity of soil enzymes and soil biota - whether due to substrate addition or in this case toxicity - are largely confined to enzymatic hotspot areas.

Characterization of an antimony-resistant fungus Sarocladium kiliense ZJ-1 and its potential as an antimony bio-remediator

Antimony (Sb) is a toxic metalloid widely distributed in the natural environments. Microorganisms, especially fungi, could serve as ideal biomaterials for bioremediation of Sb-polluted soils and waters. In this study, we isolated an antimony-resistant fungus, Sarocladium kiliense ZJ-1, from a slag sample collected in Xikuangshan Sb mine in P. R. China. ZJ-1 showed an extremely high resistance to Sb, with a MIC level of > 175 mM for arsenite [Sb(Ⅲ)] and 40 mM for arsenate [Sb(V)]. Whole genomic analysis identified multiple Sb (Ⅲ)- and/or As(Ⅲ)-resistant genes on ZJ-1's genome, which may partially explain its hyper-resistance to Sb. The potential of ZJ-1 in removing Sb from Sb(Ⅲ) or Sb(V) solutions was also quantified. The average biosorption capacity of ZJ-1 for Sb(Ⅲ) and Sb(V) is 635.14 mg/g and 149.65 mg/g, respectively, in Sb aqueous solutions with an initial concentration of 2000 mg/L (16.43 mM). Besides, almost 99% of Sb(Ⅲ) in the growing system was removed with an initial concentration of 500 mg/L (4.11 mM). Furthermore, Fourier transformation infrared spectroscopy (FT-IR) and X-ray photoelectron spectroscopy (XPS) were used to probe the Sb adsorption mechanism on ZJ-1, and -OH, -NH2, -COOH, C-O and C-O-C were found to be the main surface functional groups of ZJ-1 cells to adsorb Sb.

Archaea are better adapted to antimony stress than their bacterial counterparts in Xikuangshan groundwater

Archaea are important ecological components of microbial communities in various environments, but are currently poorly investigated in antimony (Sb) contaminated groundwater particularly on their ecological differences in comparison with bacteria. To address this issue, groundwater samples were collected from Xikuangshan aquifer along an Sb gradient and subjected to 16S rRNA gene amplicon sequencing and bioinformatic analysis. The results demonstrated that bacterial communities were more susceptibly affected by elevated Sb concentration than their archaeal counterparts, and the positive stimulation of Sb concentration on bacterial diversity coincided with the intermediate disturbance hypothesis. Overall, the balance of environmental variables (Sb, pH, and EC), competitive interactions, and stochastic events jointly regulated bacterial and archaeal communities. Linear fitting analysis revealed that Sb significantly drove the deterministic process (heterogeneous selection) of bacterial communities, whereas stochastic process (dispersal limitation) contributed more to archaeal community assembly. In contract, the assembly of Sb-resistant bacteria and archaea was dominated by the stochastic process (undominated), which implied the important role of diversification and drift instead of selection. Compared with Sb-resistant microorganisms, bacterial and archaeal communities showed lower niche width, which may result from the constraints of Sb concentration and competitive interaction. Moreover, Sb-resistant archaea had a higher niche than that of Sb-resistant bacteria via investing on flexible metabolic pathways such as organic metabolism, ammonia oxidation; and carbon fixation to enhance their competitiveness. Our results offered new insights into the ecological adaptation mechanisms of bacteria and archaea in Sb-contaminated groundwater.

Heavy metal pollution triggers a shift from bacteria-based to fungi-based soil micro-food web: Evidence from an abandoned mining-smelting area

Heavy metals pose significant threats to soil biota, ultimately disrupting soil micro-food web. However, no studies have yet elucidated the impact of heavy metals on soil micro-food web. In this study, we explored the response of bacteria, fungi, nematodes, and soil micro-food web along a gradient of heavy metals in an abandoned smelting-mining area. We found that bacteria responded strongly to heavy metals, whereas fungi showed greater resistance and tolerance. Nematodes responses were less apparent. With the increasing levels of heavy metal pollution, the importance of heavy metal-tolerant organisms in micro-food webs increased significantly. For instance, the keystone bacteria in soil micro-food web shifted from copiotrophic to oligotrophic types, while the keystone nematodes shifted from to bacterial-feeding (e.g., Eucephalobus) to fungal-feeding species (e.g., Ditylenchus). Additionally, elevated heavy metal concentrations increased the proportion of fungi (e.g., Mortierellomycota), intensifying their interactions with bacteria and nematodes and causing a shift from bacteria-based to fungi-based soil micro-food web. Furthermore, heavy metal contamination induced a more complex and stable soil micro-food web. Overall, we highlight the changes in soil micro-food web as a mechanism for coping with heavy metal stress. Our study provides valuable insights into how heavy metal pollution can cause shifts in soil micro-food webs and has critical implications for enhancing our understanding of the ecological consequences of environmental pollution at the ecosystem level.

Variations in bacterial diversity and community structure in the sediments of an alkaline lake in Inner Mongolia plateau, China

Alkaline lakes are a special aquatic ecosystem that act as important water and alkali resource in the arid-semiarid regions. The primary aim of the study is to explore how environmental factors affect community diversity and structure, and to find whether there are key microbes that can indicate changes in environmental factors in alkaline lakes. Therefore, four sediment samples (S1, S2, S3, and S4) were collected from Hamatai Lake which is an important alkali resource in Ordos' desert plateau of Inner Mongolia. Samples were collected along the salinity and alkalinity gradients and bacterial community compositions were investigated by Illumina Miseq sequencing. The results revealed that the diversity and richness of bacterial community decreased with increasing alkalinity (pH) and salinity, and bacterial community structure was obviously different for the relatively light alkaline and hyposaline samples (LAHO; pH < 8.5; salinity < 20‰) and high alkaline and hypersaline samples (HAHR; pH > 8.5; salinity > 20‰). Firmicutes, Proteobacteria and Bacteriodetes were observed to be the dominant phyla. Furthermore, Acidobacteria, Actinobacteria, and low salt-tolerant alkaliphilic nitrifying taxa were mainly distributed in S1 with LAHO characteristic. Firmicutes, Clostridia, Gammaproteobacteria, salt-tolerant alkaliphilic denitrifying taxa, haloalkaliphilic sulfur cycling taxa were mainly distributed in S2, S3 and S4, and were well adapted to haloalkaline conditions. Correlation analysis revealed that the community diversity (operational taxonomic unit numbers and/or Shannon index) and richness (Chao1) were significantly positively correlated with ammonium nitrogen (r = 0.654, p < 0.05; r = 0.680, p < 0.05) and negatively correlated with pH (r = -0.924, p < 0.01; r = -0.800, p < 0.01; r = -0.933, p < 0.01) and salinity (r = -0.615, p < 0.05; r = -0.647, p < 0.05). A redundancy analysis and variation partitioning analysis revealed that pH (explanation degrees of 53.5%, pseudo-F = 11.5, p < 0.01), TOC/TN (24.8%, pseudo-F = 10.3, p < 0.05) and salinity (9.2%, pseudo-F = 9.5, p < 0.05) were the most significant factors that caused the variations in bacterial community structure. The results suggested that alkalinity, nutrient salt and salinity jointly affect bacterial diversity and community structure, in which one taxon (Acidobacteria), six taxa (Cyanobacteria, Nitrosomonadaceae, Nitrospira, Bacillus, Lactococcus and Halomonas) and five taxa (Desulfonatronobacter, Dethiobacter, Desulfurivibrio, Thioalkalivibrio and Halorhodospira) are related to carbon, nitrogen and sulfur cycles, respectively. Classes Clostridia and Gammaproteobacteria might indicate changes of saline-alkali conditions in the sediments of alkaline lakes in desert plateau.

Dopamine alleviates cadmium stress in apple trees by recruiting beneficial microorganisms to enhance the physiological resilience revealed by high-throughput sequencing and soil metabolomics

Dopamine has demonstrated promise as a stress-relief substance. However, the function of dopamine in Cd tolerance and its mechanism remains largely unknown. The current study was performed to investigate the mechanism of dopamine on alleviating apple Cd stress through regular application of CdCl2 and dopamine solution to potting soil. The results indicated that dopamine significantly reduced reactive oxygen species (ROS) and Cd accumulation and alleviated the inhibitory effect of Cd stress on the growth of apple plants through activation of the antioxidant system, enhancement of photosynthetic capacity, and regulation of gene expression related to Cd absorption and detoxification. The richness of the rhizosphere microbial community increased, and community composition and assembly were affected by dopamine treatment. Network analysis of microbial communities showed that the numbers of nodes and total links increased significantly after dopamine treatment, while the keystone species shifted. Linear discriminant analysis effect size indicated that some biomarkers were significantly enriched after dopamine treatment, suggesting that dopamine induced plants to recruit potentially beneficial microorganisms (Pseudoxanthomonas, Aeromicrobium, Bradyrhizobium, Frankia, Saccharimonadales, Novosphingobium, and Streptomyces) to resist Cd stress. The co-occurrence network showed several metabolites that were positively correlated with relative growth rate and negatively correlated with Cd accumulation, suggesting that potentially beneficial microorganisms may be attracted by several metabolites (L-threonic acid, profenamine, juniperic acid and (3β,5ξ,9ξ)-3,6,19-trihydroxyurs-12-en-28-oic acid). Our results demonstrate that dopamine alleviates Cd stress in apple trees by recruiting beneficial microorganisms to enhance the physiological resilience revealed. This study provides an effective means to reduce the harm to agricultural production caused by heavy metals.

Variance of soil bacterial community and metabolic profile in the rhizosphere vs. non-rhizosphere of native plant Rumex acetosa L. from a Sb/As co-contaminated area in China

Heavy metals (HMs) contamination poses a serious threat to soil health. However, the rhizosphere effect of native pioneer plants on the soil ecosystem remains unclear. Herein, how the rhizosphere (Rumex acetosa L.) influenced the process of HMs threatening soil micro-ecology was investigated by coupling various fractions of HMs, soil microorganisms and soil metabolism. The rhizosphere effect alleviated the HMs' stress by absorbing and reducing HMs' direct bioavailability, and the accumulation of ammonium nitrogen increased in the rhizosphere soil. Meanwhile, severe HMs contamination covered the rhizosphere effect on the richness, diversity, structure and predicted function pathways of soil bacterial community, but the relative abundance of Gemmatimonadota decreased and Verrucomicrobiota increased. The content of total HMs and physicochemical properties played a more important role than rhizosphere effect in shaping soil bacterial community. Furthermore, As was observed to have a more significant impact compared to Sb. Moreover, plant roots improved the stability of bacterial co-occurrence network, and significantly changed the critical genera. The process influenced bacterial life activity and nutrient cycling in soil, and the conclusion was further supported by the significant difference in metabolic profiles. This study illustrated that in Sb/As co-contaminated area, rhizosphere effect significantly changed soil HMs content and fraction, soil properties, and microbial community and metabolic profiles.

Response of soil microbial activities and ammonia oxidation potential to environmental factors in a typical antimony mining area

Mining, smelting and tailing deposition activities can cause metal(loid) contamination in surrounding soils, threatening ecosystems and human health. Microbial indicators are sensitive to environmental factors and have a crucial role in soil ecological risk assessment. Xikuangshan, the largest active antimony (Sb) mine in the world, was taken as the research area. The soil properties, metal(loid) contents and microbial characteristics were investigated and their internal response relationships were explored by multivariate statistical analysis. The assessment of the single pollution index and Nemerow synthetic pollution index (P_N) showed that the soils were mainly polluted by Sb, followed by Cd and As, in which sampling site S1 had a slight metal(loid) pollution and the other sampling sites suffered from severe synthetic metal(loid) pollution. The microbial characteristics were dissimilar among sampling points at different locations from the mining area according to hierarchical cluster analysis. The correlation analysis indicated that fluorescein diacetate hydrolase, acid phosphatase, soil basal respiration and microbial biomass carbon were negatively correlated with P_N, indicating their sensitivity to combined metal(loid) contamination; that dehydrogenase was positively correlated with pH; and that urease, potential ammonia oxidation and abundance of ammonia-oxidizing bacteria and archaea were correlated with N (nitrogen) contents. However, β-glucosidase activity had no significant correlations with physicochemical properties and metal(loid) contents. Principal components analysis suggested bioavailable Sb and pH were the dominant factors of soil environment in Xikuangshan Sb mining area. Our results can provide a theoretical basis for ecological risk assessment of contaminated soil.

Phylogenetic distance affects the artificial microbial consortia's effectiveness and colonization during the bioremediation of polluted soil with Cr(VI) and atrazine

Soils co-contaminated with heavy metals and organic pollutants are common and threaten the natural environment and human health. Although artificial microbial consortia have advantages over single strains, the mechanism affecting their effectiveness and colonization in polluted soils still requires determination. Here, we constructed two kinds of artificial microbial consortia from the same or different phylogenetic groups and inoculated them into soil co-contaminated with Cr(VI) and atrazine to study the effects of phylogenetic distance on consortia effectiveness and colonization. The residual concentrations of pollutants demonstrated that the artificial microbial consortium from different phylogenetic groups achieved the highest removal rates of Cr(VI) and atrazine. The removal rate of 400 mg/kg atrazine was 100%, while that of 40 mg/kg Cr(VI) was 57.7%. High-throughput sequence analysis showed that the soil bacterial negative correlations, core genera, and potential metabolic interactions differed among treatments. Furthermore, artificial microbial consortia from different phylogenetic groups had better colonization and a more significant effect on the abundance of native core bacteria than consortia from the same phylogenetic group. Our study highlights the importance of phylogenetic distance on consortium effectiveness and colonization and offers insight into the bioremediation of combined pollutants.

Soil microbial responses to simultaneous contamination of antimony and arsenic in the surrounding area of an abandoned antimony smelter in Southwest China

Soil contamination with heavy metal(loid)s may influence microbial activities in the soil, and consequently jeopardize soil health. Microbial responses to soil contamination play an important role in ecological risk assessment. This study investigated the effect of heavy metal(loid)s contamination on microbial community structure and abundance in the surrounding soil of an abandoned antimony (Sb) smelter in Qinglong county, Guizhou province, Southwest China. A total of 46 soil samples were collected from ten sampling sites (labelled as A-I, and CK) across the study area at depths of 0-2, 2-10, 10-20, 20-30, 30-40, and 40-50 cm. The soil samples were analyzed for total and bioavailable heavy metal(loid) concentrations, bacterial, fungal, and archaeal community structures, diversities, and functions, together with soil basic physicochemical properties. Much greater ecological risk of Sb and arsenic (As) was present in the surface soil (0-2 cm) compared to that in the subsoils. The activities of dominant microorganisms tended to be associated with soil pH and heavy metal(loid)s (i.e., Sb, As, lead (Pb), cadmium (Cd), and chromium (Cr)). Bacteria associated with IMCC26256, Rhizobiales, Burkholderiales, and Gaiellales, and archaea associated with Methanocellales were estimated to be tolerant to high concentrations of Sb and As in the soil. In addition, the magnitude of soil microbial responses to Sb and As contamination was in the order of archaea > bacteria > fungi. In contrast to the negligible response of fungi and negative response of bacteria to Sb and As contamination, there was a strongly positive correlation between archaeal activity and total Sb and As concentrations in the soil. Our findings provide a theoretical basis for the remediation of Sb smelter-affected soil.

Antimony oxidation and whole genome sequencing of Phytobacter sp. X4 isolated from contaminated soil near a flotation site

The conversion of the more toxic Sb(III) into less toxic Sb(V) is an effective strategy for the treatment of antimony-contaminated sites. In this study, a strain, Phytobacter sp. X4, which can tolerate high concentrations of antimony and can use nitrate as an electron acceptor for Sb(III) oxidation under anaerobic conditions, was isolated from the deep soil of an antimony mine flotation tailing. Unlike other antimony oxidizing bacteria, X4 oxidized better under high Sb(III) concentration, and the oxidation efficiency of 10 mM Sb(III) reached the maximum at 110 h with 61.8 %. Kinetic study showed X4 yielded a V_max of 1.093 μM∙min^-1 and a K_m of 718.2 μM. The genome of Phytobacter sp. X4 consists of a complete circular chromosome and two plasmids. In addition, X4 had more metal(loid)s resistance genes and highly expressed genes than other Phytobacter spp., reflecting its stronger adaptive advantage in harsh survival environments. We also analyzed the origin and evolution of arsB, arsC, and arsH, which may have been transferred horizontally from other species. iscR and arsH may have an important contribution to Sb(III) oxidation. Thus, Phytobacter sp. X4 has a good ability to remediate high antimony-contaminated sites and can be applied to an anaerobic environment.

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.

Heavy metals reshaping the structure and function of phylloplane bacterial community of native plant Tamarix ramosissima from Pb/Cd/Cu/Zn smelting regions

Heavy metal (HM) is noxious element that cannot be biodegraded, thus accumulating in the environment and posing a serious threat to the ecology. Plant phylloplane harbors diverse microbial communities that profoundly influence ecosystem functioning and host health. With more HM accumulating around smelters, native plants and microbes in various habitats tend to suffer from HM. However, the response of phylloplane bacteria of native plants to HM remains unclear. Thus, this study aimed to explain the response of Tamarix ramosissima, a phylloplane bacterial community to HM as well as the effect of the process on host growth in situ by investigating the potential source of HM and bacterial community shift. Results showed that, in most cases, the contaminated site with high HM level caused more accumulation of HM in phylloplane and leaves. Moreover, HM in the phylloplane was not from the internal transport of the plant but it could be due to the wind action or rains. Bacteria in phylloplane may have come from the soil due to their strong positive correlation with corresponding soil at the genus level. High HM level inhibited the relative abundance of dominant bacteria, increased the diversity and species richness of bacterial community in phylloplane, and induced more special bacteria to maintain higher productivity of the host plant, for which, Cu and Pb were the major contributors. Meanwhile, bacteria in phylloplane showed a universal positive correlation in the co-occurrence network, which showed less stability than that in corresponding soil in the smelting region, and it is helpful to regulate the growth of plants more rapidly. Nearly 25% of KEGG pathways were modulated by high HM level and bacterial function tended to stabilize HM to avoid the potential process of leaf absorption. The study illustrated that HM in phylloplane played an important role in shaping the bacterial community of phylloplane as compared to HM in leaves or phyllosphere, and the resulting increase of diversity and richness of bacterial community and special bacteria further maintained the growth of the host plant suffering from HM stress.

Biotic interactions contribute more than environmental factors and geographic distance to biogeographic patterns of soil prokaryotic and fungal communities

Recent studies have shown distinct soil microbial assembly patterns across taxonomic types, habitat types and regions, but little is known about which factors play a dominant role in soil microbial communities. To bridge this gap, we compared the differences in microbial diversity and community composition across two taxonomic types (prokaryotes and fungi), two habitat types (Artemisia and Poaceae) and three geographic regions in the arid ecosystem of northwest China. To determine the main driving factors shaping the prokaryotic and fungal community assembly, we carried out diverse analyses including null model, partial mantel test and variance partitioning analysis etc. The findings suggested that the processes of community assembly were more diverse among taxonomic categories in comparison to habitats or geographical regions. The predominant driving factor of soil microbial community assembly in arid ecosystem was biotic interactions between microorganisms, followed by environmental filtering and dispersal limitation. Network vertex, positive cohesion and negative cohesion showed the most significant correlations with prokaryotic and fungal diversity and community dissimilarity. Salinity was the major environmental variable structuring the prokaryotic community. Although prokaryotic and fungal communities were jointly regulated by the three factors, the effects of biotic interactions and environmental variables (both are deterministic processes) on the community structure of prokaryotes were stronger than that of fungi. The null model revealed that prokaryotic community assembly was more deterministic, whereas fungal community assembly was structured by stochastic processes. Taken together, these findings unravel the predominant drivers governing microbial community assembly across taxonomic types, habitat types and geographic regions and highlight the impacts of biotic interactions on disentangling soil microbial assembly mechanisms.

Response of soil protists to antimony and arsenic contamination

Microorganisms can mediate antimony (Sb) and arsenic (As) transformation and thus change their mobility and toxicity. Having similar geochemical behavior, Sb and As are generally considered to exert similar environmental pressure on microbiome. However, it needs further validation, especially for protists. In this study, the responses of protistan communities to Sb and As were investigated by collecting soils from Xikuangshan Sb mine and Shimen As mine in China. Antimony and As contamination taxonomically and functionally (consumer and phototroph) changed the alpha and beta diversities of protistan communities, but exerted different impacts on the parasitic community. Based on multiple statistical tools, As contamination had a greater impact on protistan communities than Sb. The ecological networks of highly contaminated sites were less complex but highly positively connected compared to less contaminated sites. High As contamination raised the ratio of consumers and decreased the ratio of phototrophs in ecological networks, while the opposite tendency was observed in Sb contaminated soils. High Sb and As contamination enriched different keystone taxa resistant to Sb and As. These results demonstrate that protistan community respond differently to Sb and As.

Structural and functional characteristics of soil microbial communities in response to different ecological risk levels of heavy metals

Objective

The potential ecological risk index (RI) is the most commonly used method to assess heavy metals (HMs) contamination in soils. However, studies have focused on the response of soil microorganisms to different concentrations, whereas little is known about the responses of the microbial community structures and functions to HMs at different RI levels.

Methods

Here, we conducted soil microcosms with low (L), medium (M) and high (H) RI levels, depending on the Pb and Cd concentrations, were conducted. The original soil was used as the control (CK). High-throughput sequencing, qPCR, and Biolog plate approaches were applied to investigate the microbial community structures, abundance, diversity, metabolic capacity, functional genes, and community assembly processes.

Result

The abundance and alpha diversity indices for the bacteria at different RI levels were significantly lower than those of the CK. Meanwhile, the abundance and ACE index for the fungi increased significantly with RI levels. Acidobacteria, Basidiomycota and Planctomycetes were enriched as the RI level increased. Keystone taxa and co-occurrence pattern analysis showed that rare taxa play a vital role in the stability and function of the microbial community at different RI levels. Network analysis indicates that not only did the complexity and vulnerability of microbial community decrease as risk levels increased, but that the lowest number of keystone taxa was found at the H level. However, the microbial community showed enhanced intraspecific cooperation to adapt to the HMs stress. The Biolog plate data suggested that the average well color development (AWCD) reduced significantly with RI levels in bacteria, whereas the fungal AWCD was dramatically reduced only at the H level. The functional diversity indices and gene abundance for the microorganisms at the H level were significantly lower than those the CK. In addition, microbial community assembly tended to be more stochastic with an increase in RI levels.

Conclusion

Our results provide new insight into the ecological impacts of HMs on the soil microbiome at different risk levels, and will aid in future risk assessments for Pb and Cd contamination.

A poisoned apple: First insights into community assembly and networks of the fungal pathobiome of healthy-looking senescing leaves of temperate trees in mixed forest ecosystem

Despite the abundance of observations of foliar pathogens, our knowledge is severely lacking regarding how the potential fungal pathobiome is structured and which processes determine community assembly. In this study, we addressed these questions by analysing the potential fungal pathobiome associated with the senescing leaves and needles of 12 temperate tree species. We compared fungal plant pathogen load in the senescing leaves/needles and demonstrated that healthy-looking leaves/needles are inhabited by diverse and distinct fungal plant pathogens. We detected 400 fungal plant pathogenic ASVs belonging to 130 genera. The fungal plant pathogenic generalist, Mycosphaerella, was found to be the potential most significant contributor to foliar disease in seedlings. The analyses of assembly process and co-occurrence network showed that the fungal plant pathogenic communities in different tree types are mainly determined by stochastic processes. However, the homogenising dispersal highly contributes in broadleaf trees, whereas ecological drift plays an important role in coniferious trees. The deterministic assembly processes (dominated by variable selection) contributed more in broadleaf trees as compared to coniferous trees. We found that pH and P level significantly corresponded with fungal plant pathogenic community compositions in both tree types. Our study provides the first insight and mechanistic understanding into the community assembly, networks, and complete taxonomy of the foliar fungal pathobiome in senescing leaves and needles.

Disentangling biogeographic and underlying assembly patterns of fungal communities in metalliferous mining and smelting soils

Elucidating community assembly and their relevance to environmental variables are fundamental for understanding microbial diversity and functioning in terrestrial ecosystems, yet the geographical diversity and assembly patterns of the fungal community in metalliferous ecospheres associated with mining and smelting activities have received penurious understandings. Here, the fungal communities collected from three groups of soils around the mining and smelting sites were profiled by Internal Transcribed Spacer (ITS) sequencing, in order to understand the geographical distributions of fungal community diversities, structures, compositions, assembly processes and the occurrence patterns. The results suggested obvious biogeographic distribution patterns of fungal compositions among the three groups of soils. Among them, 15 fungal phyla including Ascomycota, Basidiomycota and Mortierellomycota were recognized across the samples. 12 abundant classes showing significantly different in relative abundances among the three groups of soils. Total metal(loid)s and level significantly decreased the fungal abundances and diversities. The community similarity demonstrated distance-decay pattern among the three sites. Metal(loid)s explained relatively higher fungal community variations (4.16 %) relative to other factors (1.89 %) and geography (1.21 %), though 83.32 % of the variations could not be explained. Stochastic dispersal limitation and undominated fraction were dominated relative to deterministic heterogeneous selection in total and individual site, respectively. These results highlighted the stochastic processes in governing the biogeography of fungal communities in mining and smelting ecospheres.

Plant traits and community composition drive the assembly processes of abundant and rare fungi across deserts

The difference in community assembly mechanisms between rare and abundant fungi in deserts remains unknown. Hence, we compared the distribution patterns of abundant and rare fungi, and assessed the factors driving their assembly mechanisms across major vegetation types (shrubby desert, semi-shrubby and dwarf semi-shrubby desert, dwarf semi-arboreous desert, and shrubby steppe desert) of Chinese deserts. We assessed abundant and rare fungal subcommunities base on the sequencing data of fungal ITS data. Abundant fungal assembly was more affected by neutral processes than the rare. Null model and VPA analysis indicated that heterogeneous selection dominated rare sub-communities, whereas abundant fungal assembly was mainly determined by heterogeneous selection, dispersal limitation and other, unknown processes together. As a result, abundant sub-communities exhibited a higher species turnover rate than the rare. Hierarchical partitioning analysis indicated that soil conditions and plant attributes drove the assembly processes of abundant and rare fungi, respectively. Meanwhile, the relative strength of different assembly processes differed significantly among four vegetation types. In addition, we found that plant functional traits and composition played more critical roles in shaping the assembly processes of rare fungi than those of abundant fungi. Taken together, our findings collectively suggest that rare and abundant fungi exhibit differential ecological patterns that are driven by distinct assembly processes in deserts. We emphasize that the assembly processes of abundant and rare fungi are dependent on different abiotic and biotic factors in desert ecosystems.

Rhizosphere Microbial Communities and Geochemical Constraining Mechanism of Antimony Mine Waste-Adapted Plants in Southwestern China

Antimony (Sb) and arsenic (As) are two hazardous metalloid elements, and the biogeochemical cycle of Sb and As can be better understood by studying plant rhizosphere microorganisms associated with Sb mine waste. In the current study, samples of three types of mine waste—Sb mine tailing, waste rocks, and smelting slag—and associated rhizosphere microorganisms of adapted plants were collected from Qinglong Sb mine, southwest China. 16S rRNA was sequenced and used to study the composition of the mine waste microbial community. The most abundant phylum in all samples was Proteobacteria, followed by Bacteroidota, Acidobacteriota, and Actinobacteriota. The community composition varied among different mine waste types. Gammaproteobacteria was the most abundant microorganism in tailings, Actinobacteria was mainly distributed in waste rock, and Saccharimonadia, Acidobacteriae, and Ktedonobacteria were mainly present in slag. At the family level, the vast majority of Hydrogenophilaceae were found in tailings, Ktedonobacteraceae, Chthoniobacteraceae, and Acidobacteriaceae (Subgroup 1) were mostly found in slag, and Pseudomonadaceae and Micrococcaceae were mainly found in waste rock. Actinobacteriota and Arthrobacter are important taxa for reducing heavy metal(loid) mobility, vegetation restoration, and self-sustaining ecosystem construction on antimony mine waste. The high concentrations of Sb and As reduce microbial diversity.