Structure and diversity of fungal communities in long-term copper-contaminated agricultural soil

Response patterns of the microbiome during hexavalent chromium remediation by Tagetes erecta L

Chromium pollution, particularly hexavalent chromium [Cr(VI)], may threaten the environment and human health. This study investigated the potential of Tagetes erecta L. (Aztec marigold) for phytoremediation of soil contaminated with Cr(VI), and focused on the effects of varying concentrations of Cr(VI) on both the physicochemical properties of soil and microbiome of Tagetes erecta L. We observed that Tagetes erecta L. showed tolerance to Cr(VI) stress and maintained normal growth under these conditions, as indicated by bioconcentration factors of 0.33-0.53 in shoots and 0.39-0.70 in roots. Meanwhile, the structure and diversity of bacterial communities were significantly affected by Cr(VI) pollution. Specifically, Cr(VI) had a more significant effect on the microbial community structure in the endophytic of Tagetes erecta L. than in the rhizosphere (p < 0.05). The genera Devosia and Methylobacillus were positively correlated with Cr(VI) concentrations. Biomarkers such as Bacilli and Pseudonocardia were identified under the different Cr(VI)-contaminated treatments using LEfSe. In addition, the interaction and stability of the endophytic microbiome were enhanced under Cr(VI) stress. This study explored the interactions between heavy metals, microorganisms, and plants, providing valuable insights for developing in situ bioremediation of Cr(VI)-contaminated soils.

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.

Chitosan- and gallic acid-based (NPF) displayed antibacterial activity against three Pseudomonas spp. plant pathogens and boosted systemic acquired resistance in kiwifruit and olive plants

BACKGROUD

Pseudomonas syringae pv. actinidiae (Psa), P. syringae pv. tomato (Pst) and P. savastanoi pv. savastanoi (Psav) are bacterial plant pathogens with worldwide impact that are mainly managed by the preventive application of cupric salts. These are dangerous for ecosystems and have favoured the selection of resistant strains, so they are candidates to be replaced in the next few years. Thus, there is an urgent need to find efficient and bio-based solutions to mitigate these bacterial plant diseases. Nanotechnology could represent an innovative way to control plant diseases, providing alternative solutions to the agrochemicals traditionally employed, thanks to the formulation of the so-called third-generation and nanotechnology-based agrochemicals.

RESULTS

In this work, a novel nanostructured formulation (NPF) composed of cellulose nanocrystals (CNC) as carrier, high amylose starch (HAS) as excipient, and chitosan (CH) and gallic acid (GA) as antimicrobials, was tested at 2% in vitro and in vivo with respect to the three different Pseudomonas plant pathogens. In vitro agar assays demonstrated that the NPF inhibited ≤80% Psa, Pst and Psav. Moreover, the NPF did not decrease biofilm synthesis and it did not influence bacterial cells flocculation and adhesion. On plants, the NPF displayed complete biocompatibility and boosted the transcript levels of the major systemic acquired resistance responsive genes in kiwifruit and olive plants.

CONCLUSION

This works provides novel and valuable information regarding the several modes-of-action of the novel NPF, which could potentially be useful to mitigate Psa, Pst and Psav infections even in organic agriculture. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

The use of copper as plant protection product contributes to environmental contamination and resulting impacts on terrestrial and aquatic biodiversity and ecosystem functions

Copper-based plant protection products (PPPs) are widely used in both conventional and organic farming, and to a lesser extent for non-agricultural maintenance of gardens, greenspaces, and infrastructures. The use of copper PPPs adds to environmental contamination by this trace element. This paper aims to review the contribution of these PPPs to the contamination of soils and waters by copper in the context of France (which can be extrapolated to most of the European countries), and the resulting impacts on terrestrial and aquatic biodiversity, as well as on ecosystem functions. It was produced in the framework of a collective scientific assessment on the impacts of PPPs on biodiversity and ecosystem services in France. Current science shows that copper, which persists in soils, can partially transfer to adjacent aquatic environments (surface water and sediment) and ultimately to the marine environment. This widespread contamination impacts biodiversity and ecosystem functions, chiefly through its effects on phototrophic and heterotrophic microbial communities, and terrestrial and aquatic invertebrates. Its effects on other biological groups and biotic interactions remain relatively under-documented.

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

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

Copper and cadmium co-contamination affects soil bacterial taxonomic and functional attributes in paddy soils

Microorganisms inhabiting heavy metal-contaminated soils have evolved specific metabolic capabilities to survive, which has the potential for effective bioremediation. However, the ecological consequence of copper (Cu) and cadmium (Cd) on bacterial taxonomic and functional attributes of rice field remains unclear. Here, we selected paddy soils along a polluted river in southern China to evaluate the role of Cu and Cd contaminant fractions in regulating bacterial co-occurrence patterns. We also assessed the effects of these heavy metal fractions on the relative abundance of functional genes using shotgun metagenomic analysis. Soil Cu and Cd concentrations in paddy soils gradually decreased from upstream to downstream of the river, and had a greater impact on bacterial communities and metabolic potentials than soil general properties. Soil Cu and Cd contamination led to drastic changes in the cumulative relative abundance of ecological modules in bacterial co-occurrence networks. Bacteria associated with AD3, HSB_OF53-F07 (both belonging to Chloroflexi), Rokubacteriales, and Nitrospira were identified as tolerant to Cu and Cd contamination. The Cu and Cd contaminant fractions were positively correlated with the genes involved in metal resistance, carbon (C) fixation, nitrification, and denitrification, but negatively correlated with the genes related to nitrogen (N) fixation. These results indicated that soil Cu and Cd pollution not only enriched metal resistant genes, but also affected genes related to microbial C and N cycling. This is critical for facilitating microbiome bioremediation of metal-contaminated paddy soils.

Response of soil fungal community to chromium contamination in agricultural soils with different physicochemical properties

Chromium (Cr) contamination has been of great concern in agricultural soil health due to its persistence, toxicity and bioaccumulation. Fungi, as an essential regulator of soil remediation and biochemical processes, had an unclear response to Cr contamination. In this study, the composition, diversity and interaction mechanisms of fungal communities in agricultural soils from ten different provinces of China were investigated in order to elucidate the fungal community response to varying soil properties and Cr concentrations. The results showed that high concentrations of Cr led to substantial alterations in the fungal community composition. The complex soil properties had a far greater impact on the fungal community structure than the single factor of Cr concentration, with soil available phosphorus (AP) and pH being most influential. Function predictions based on FUNGuild indicated that high concentrations of Cr have a significant impact on certain functional groups of fungi, including mycorrhizal fungi and plant saprotroph. The fungal community tended to resist Cr stress by enhancing interactions and clustering among network modules, while generating new keystone taxa. This study allowed insights into the response of soil fungal community to Cr contamination in different agricultural soils from different provinces and provided a theoretical basis for soil Cr ecological risk assessment and the development of bioremediation techniques for Cr-contaminated soils.

Insights into the responses of fungal taxonomy and function to different metal(loid) contamination levels

Fungi possess prominent tolerance and detoxification capacities in highly metal(loid)-polluted systems, yet little is known about their responding behaviors under different contamination conditions. Here, we systematically investigated the structure and function profiles of fungal communities in an abandoned reservoir mainly contaminated by multiple metal(loid)s such as Al, Be, Cd, Co, Cr, and Cu. This abandoned reservoir consisted of three distinct zones, i.e., Zone I with the shortest deprecation time and the highest metal(loid) contamination; Zone II with the medium deprecation time and medium metal(loid) contamination; and Zone III with the longest abandonment time and the lowest metal(loid)contamination. The lowest pH and the highest contents of OM, TN, and TP were also observed for the high-contamination Zone I, followed by the moderate-contamination Zone II and the low-contamination Zone III. Fungal biodiversity was found to be robust and dominated by many endurable genera in Zone I, and notable cooperative relationships among fungal species facilitated their viability and prosperity under severe metal(loid) contaminations. Differently, the lowest biodiversity and fragile co-occurrence network were identified in Zone II. As metal(loid) contaminations reduced from Zone I to Zone III, dominant fungal functions gradually changed from undefined saprotroph guild to parasites or pathogens of plant-animal (i.e. animal pathogen, endophyte, and plant pathogen). Moreover, metal(loid)s combined with physicochemical properties jointly mediated the fungal taxonomic and functional responses to different metal(loid) contamination levels. Overall, this study not only broadens the understanding of taxonomic and functional repertoires of fungal communities under different metal(loid) contaminated conditions, but also highlights the crucial contributions of specific fungi to bioremediation and management in varying metal(loid)-polluted environments.

Variations of microbiota in three types of typical military contaminated sites: Diversities, structures, influence factors, and co-occurrence patterns

Contamination with energetic compounds (ECs) is common in military sites and poses a great risk to the environment and human health. However, its effects on the soil bacterial communities remain unclear. This study assessed the variations of bacterial communities, co-occurrence patterns, and their influence factors in three types of typical military-contaminated sites (artillery range, military-industrial site, and ammunition destruction site). The results showed that the most polluted sites were ammunition destruction sites, followed by military-industrial sites, whereas pollution in the artillery ranges was minimal. The average concentrations of ECs including 2,4,6-trinitrotoluene (TNT), hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) in the study sites ranged 120-1.67 × 10⁵, 20-7.20 × 10⁴, and 180-2.38 × 10⁵ μg/kg, respectively. Bacterial diversity and community structure in military-industrial and ammunition destruction sites were significantly changed, but not in artillery ranges. TNT, pH, and soil moisture are the critical factors affecting bacterial communities in contaminated military sites. Co-occurrence network analysis indicated that the pressure of ECs affected bacterial interactions and microbiota function. Our findings provide new insights into the variations in bacterial communities in EC-contaminated military sites and references for the bioremediation of ECs.

Clomazone impact on fungal network complexity and stability

Introduction

Soil fungal network composition and stability are important for soil functions, but there is less understanding of the impact of clomazone on network complexity and stability.

Methods

In this work, two agricultural soils were used to investigate the impact of clomazone on fungal network complexity, composition, and stability. The two soils were treated with clomazone solution (0, 0.8, 8, and 80  mg kg^-1) and kept in an incubator.

Results and Discussion

Under the influence of clomazone, the fungal network nodes were decreased by 12-42; however, the average degree was increased by 0.169-1.468 and fungal network density was increased by 0.003-0.054. The keystone nodes were significantly changed after clomazone treatment. Network composition was also impacted. Specifically, compared with control and clomazone treatments in both soils, the shared edges were fewer than 54 in all comparisons, and network dissimilarity was 0.97-0.98. These results suggested that fungal network composition was significantly impacted. The network robustness was increased by 0.0018-0.0209, and vulnerability was decreased by 0.00018-0.00059 in both soils, which indicated that fungal network stability was increased by clomazone. In addition, the functions of network communities were also changed in both soils. These results indicated that clomazone could significantly impact soil fungal networks.

Community response of soil microorganisms to combined contamination of polycyclic aromatic hydrocarbons and potentially toxic elements in a typical coking plant

Both polycyclic aromatic hydrocarbons (PAHs) and potentially toxic elements (PTEs) of coking industries impose negative effects on the stability of soil ecosystem. Soil microbes are regarded as an essential moderator of biochemical processes and soil remediation, while their responses to PAHs-PTEs combined contamination are largely unknown. In the present study, soil microbial diversity and community composition in the typical coking plant under the chronic co-exposure of PAHs and PTEs were investigated and microbial interaction networks were built to reveal microbial co-occurrence patterns. The results indicated that the concentrations of PAHs in the soil inside the coking plant were significantly higher than those outside the plant. The mean concentration of ∑16PAHs was 2894.4 ng·g^-1, which is 5.58 times higher than that outside the plant. The average Hg concentration inside the coking plant was 22 times higher than the background value of Hebei province. The soil fungal community inside the coking plant showed lower richness compared with that of outside community, and there are significant difference in the bacterial and fungal community composition between inside and outside of coking plant (p < 0.01). Predicted contribution of different environmental factors to each dominant species based on random forest identified 20 and 25 biomarkers in bacteria and fungi, respectively, that were highly sensitive to coking plant soil in operation, such as Betaproteobacteria，Sordariomycetes and Dothideomycetes. Bacterial and fungal communities were shaped by the soil chemical properties (pH), PTEs (Hg), and PAHs together in the coking plant soils. Furthermore, the bacterial and fungal interaction patterns were investigated separately or jointly by intradomain and interdomain networks. Competition is the main strategy based on the co-exclusion pattern in fungal community, and the competitive relationship inside the coking plant is more complex than that outside the plant. In contrast, cooperation is the dominant strategy in bacterial networks based on the co-occurrence pattern. The present study provided insights into microbial response strategies and the interactions between bacteria and fungi under long-term combined contamination.

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.

Responses of soil fungal taxonomic attributes and enzyme activities to copper and cadmium co-contamination in paddy soils

Excess heavy metals, especially copper (Cu) and cadmium (Cd), are common in paddy soils in the red soil hilly areas of southern China. Microorganisms are regulators of soil organic matter accumulation and pollutant transformation. Clarifying the effects of Cu and Cd accumulation on microbial community composition and function is a prerequisite for bioremediation of paddy soil contamination. However, it remains unclear how Cu and Cd contamination affects soil fungal taxonomic attributes and microbial-mediated biogeochemical processes in paddy soils. Here, soil heavy metals, fungal community composition, and soil enzyme activities were determined in paddy fields downstream of a typical mining area in southern China, and the effects of Cu and Cd co-contamination on fungal community diversity and co-occurrence networks, as well as the associations between them were assessed. The concentrations of Cu and Cd in paddy soils decreased from upstream to downstream of the river, and were positively correlated with the Shannon index of fungal communities. Soil Cu and Cd concentrations exhibited a greater impact on the structure and assembly of fungal communities than soil general properties. Increases in soil Cu and Cd concentrations were correlated with drastic changes in the cumulative relative abundance of ecological clusters in fungal co-occurrence networks. Soil Cu and Cd concentrations were positively correlated with the relative abundances of Eurotiomycetes, Pezizomycetes, Ustilaginomycetes, and Kickxellomycetes, respectively, whereas negatively correlated with hydrolase activities related to carbon, nitrogen, and phosphorus cycles. These results confirmed in the field that long-term Cu and Cd enrichment significantly altered the structure and diversity of fungal communities in the subtropical paddy soils, thereby affecting soil nutrient transformation and organic matter accumulation. This can also provide a basis for the bioremediation of heavy metal pollution in paddy soils.

Characterization of soil microbial community activity and structure for reducing available Cd by rice straw biochar and Bacillus cereus RC-1

The combination of biochar and specific bacteria has been widely applied to remediate Cadmium-contaminated soil. But little is known about how such composites affect the dynamic distribution of metal fractions. This process is accompanied by the alternations of soil properties and microbial community structures. Composite of rice straw biochar and Bacillus cereus RC-1 were applied to investigate its impacts on Cd alleviation and soil microbial diversity and structure. The bacterial/biochar composite treatment decreased the fraction of HOAc-extractable Cd by 38.82%, and increased residual Cd by 23.95% compared to the untreated control. Moreover, compared with the untreated control, the composite treatment significantly increased the soil pH by about 1.5 units, and the activities of catalase, urease and invertase enzymes were increased by 42.39%, 30.50% and 31.20%, respectively. Composite treatment increased soil bacterial and fungal alpha diversity, the relative abundance of Bacillus, Streptomyces, Arthrobacter, and Aspergillus species were also increased. Mantel test and correlation analysis indicated that the effects associated with fungal communities in influencing soil properties were lower than that those of bacterial communities by different treatment. Aggregated boosted tree (ABT) models analysis showed that soil chemical proprieties (as determined by SOM, CEC, AN, etc.,) contributed over 50% of the changes in bacterial and fungal communities by the composite treatment. The co-occurrence network results showed that all treatments enhanced the correlation between OUT groups and improved the possible relationships in the bacterial and fungal communities, especially the interrelationships between bacteria and fungi after the Cd fractions stabilized. These findings provide a new insight to optimal strategies for the remediation of Cd-contaminated soil.

Contamination with multiple heavy metals decreases microbial diversity and favors generalists as the keystones in microbial occurrence networks

Soil contamination with multiple heavy metals poses threats to human health and ecosystem functioning. Using the Nemerow pollution index, which considers the effects of multiple heavy metals, we compared the diversity and composition of bacteria, fungi and protists and their potential interactions in response to a multi-metal contamination gradient. Multi-metal contamination significantly altered the community composition of bacteria, fungi and protists, and the degree of alteration increased with increasing severity of contamination. The alpha-diversity of bacteria, fungi and protists significantly decreased with increasing contamination level. The dominant generalists, found in all soil samples, were Gammaproteobacteria, Chloroflexi and Bacillus sp, whereas the dominant specialists were Anaerolineaceae, Entoloma sp. and Sandonidae_X sp. The relative abundances of generalists were positively correlated, whereas those of specialists were negatively correlated, with the Nemerow pollution index. In addition, the complexity of the microbial co-occurrence network increased with increasing contamination level. Generalists, rather than specialists, were the keystones in the microbial co-occurrence network and played a crucial role in adaptation to multi-metal contamination through enhanced potential interactions within the entire microbiome. Our results provide insights into the ecological effects of multi-metal contamination on the soil microbiome and will help to develop bio-remediation technologies for contaminated soils.

Do the Reclaimed Fungal Communities Succeed Toward the Original Structure in Eco-Fragile Regions of Coal Mining Disturbances? A Case Study in North China Loess—Aeolian Sand Area

Mining activity has caused serious environmental damage, particularly for soil ecosystems. How the soil fungal community evolves in mine reclamation and what are the succession patterns of molecular ecological networks still needs to be studied in depth. We used high-throughput sequencing to explore the changes in soil fungal communities, molecular ecological networks, and interactions with soil environmental factors in five different ages (the including control group) during 14 years of reclamation in eco-fragile mines. The results showed that the abundance and diversity of soil fungi after 14 years of reclamation were close to, but still lower than, those in the undisturbed control area, but the dominant phylum was Ascomycota. Soil nitrate-N, C/N ratio, pH, and water content significantly affected the fungal community with increasing reclamation ages. Moreover, we found that Mortierellomycota, despite its high relative abundance, had little significant connectivity with other species in the molecular ecological network. Fungal molecular ecological networks evolve with increasing ages of reclamation, with larger modules, more positive connections, and tighter networks, forming large modules of more than 60 nodes by age 9. The large modules were composed mainly of Ascomycota and Basidiomycota, which can form mycorrhiza with plant roots, and are not only capable of degrading pollution but are also “encouraged” by most (more than 64%) physicochemical factors in the soil environment. The results can provide a basis for scientific mine ecological restoration, especially for eco-fragile regions.