Integrated metagenomics and molecular ecological network analysis of bacterial community composition during the phytoremediation of cadmium-contaminated soils by bioenergy crops

High levels of cadmium altered soil archaeal activity, assembly, and co-occurrence network in volcanic areas

Soil microbial communities are essential to biogeochemical cycles. However, the responses of microorganisms in volcanic soil with high heavy metal levels remain poorly understood. Here, two areas with high levels of cadmium (Cd) from the same volcano were investigated to determine their archaeal composition and assembly. In this study, the Cd concentrations (0.32-0.38 mg/ kg) in the volcanic soils exceeded the standard risk screening values (GB15618-2018) and correlated with archaeal communities strongly (P < 0.05). Moreover, the area with elevated levels of Cd (periphery) exhibited a greater diversity of archaeal species, albeit with reduced archaeal activity, compared to the area with lower levels of Cd (center). Besides, stochastic processes mainly governed the archaeal communities. Furthermore, the co-occurrence network was simplest in the periphery. The proportion of positive links between taxa increased positively with Cd concentration. Moreover, four keystone taxa (all from the family Nitrososphaeraceae) were identified from the archaeal networks. In its entirety, this study has expanded our comprehension of the variations of soil archaeal communities in volcanic areas with elevated cadmium levels and serves as a point of reference for the agricultural development of volcanic soils in China.

Plant growth-promoting bacteria improve the Cd phytoremediation efficiency of soils contaminated with PE-Cd complex pollution by influencing the rhizosphere microbiome of sorghum

Composite pollution by microplastics and heavy metals poses a potential threat to the soilplant system and has received increasing attention. Plant growth-promoting bacteria (PGPB) have good application potential for the remediation of combined microplastic and heavy metal pollution, but few related studies exist. The present study employed a pot experiment to investigate the effects of inoculation with the PGPB Bacillus sp. SL-413 and Enterobacter sp. VY-1 on sorghum growth and Cd accumulation under conditions of combined cadmium (Cd) and polyethylene (PE) pollution. Cd+PE composite contamination led to a significant reduction in sorghum length and biomass due to increased toxicity. Inoculation with Bacillus sp. SL-413 and Enterobacter sp. VY-1 alleviated the stress caused by Cd+PE complex pollution, and the dry weight of sorghum increased by 25.7% to 46.1% aboveground and by 12.3% to 45.3% belowground. Bacillus sp. SL-413 and Enterobacter sp. VY-1 inoculation increased the Cd content and accumulation in sorghum and improved the phytoremediation efficiency of Cd. The inoculation treatment effectively alleviated the nutrient stress caused by the reduction in soil mineral nutrients due to Cd+PE composite pollution. The composition of the soil bacterial communities was also affected by the Cd, Cd+PE and bacterial inoculation treatments, which affected the diversity of the soil bacterial communities. Network analyses indicated that bacterial inoculation regulated the interaction of rhizospheric microorganisms and increased the stability of soil bacterial communities. The Mantel test showed that the changes in the soil bacterial community and function due to inoculation with Bacillus sp. SL-413 and Enterobacter sp. VY-1 were important factors influencing sorghum growth and Cd remediation efficiency. The results of this study will provide new evidence for the research on joint plantmicrobe remediation of heavy metal and microplastic composite pollution.

Effects of combined microplastic and cadmium pollution on sorghum growth, Cd accumulation, and rhizosphere microbial functions

The interaction between microplastics (MPs) and cadmium (Cd) poses a threat to agricultural soil environments, and their effects on plant growth and rhizosphere microbial community functions are not yet clear. In this study, energy sorghum was used as a test plant to investigate the effects of two types of MPs, polystyrene (PS) and polyethylene (PE), at different particle sizes (13 μm, 550 μm) and concentrations (0.1%, 1% w/w), and Cd, as well as their interactions, on the growth of sorghum in a soil-cultivation pot experiment. The results showed that the combined effects of MP and Cd pollution on the dry weight and Cd accumulation rate in sorghum varied depending on the type, concentration, and particle size of the MPs, with an overall trend of increasing stress from combined pollution with increasing Cd content and accumulation. High-throughput sequencing analysis revealed that combined MP and Cd pollution increased bacterial diversity, and the most significant increase was observed in the abundance-based coverage estimator (ACE), Shannon, and Sobs indices in the 13 μm 1% PS+Cd treatment group. Metagenomic analysis based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways revealed that 19 groups of metabolic pathways, including microbial metabolism and methane metabolism, differed significantly under combined MP and Cd pollution. Hierarchical clustering results indicated that Cd treatment and combined MP and Cd treatment affected the abundances of sorghum rhizosphere soil nitrogen (N) and phosphorus (P) cycling genes and that the type of MP present was an important factor affecting N and P cycling genes. The results of this study provide a basis for exploring the toxic effects of combined MP and Cd pollution and for conducting soil environmental risk assessments.

Plant Growth-Promoting Bacteria Influence Microbial Community Composition and Metabolic Function to Enhance the Efficiency of Hybrid pennisetum Remediation in Cadmium-Contaminated Soil

The green and efficient remediation of soil cadmium (Cd) is an urgent task, and plant-microbial joint remediation has become a research hotspot due to its advantages. High-throughput sequencing and metabolomics have technical advantages in analyzing the microbiological mechanism of plant growth-promoting bacteria in improving phytoremediation of soil heavy metal pollution. In this experiment, a pot trial was conducted to investigate the effects of inoculating the plant growth-promoting bacterium Enterobacter sp. VY on the growth and Cd remediation efficiency of the energy plant Hybrid pennisetum. The test strain VY-1 was analyzed using high-throughput sequencing and metabolomics to assess its effects on microbial community composition and metabolic function. The results demonstrated that Enterobacter sp. VY-1 effectively mitigated Cd stress on Hybrid pennisetum, resulting in increased plant biomass, Cd accumulation, and translocation factor, thereby enhancing phytoremediation efficiency. Analysis of soil physical-chemical properties revealed that strain VY-1 could increase soil total nitrogen, total phosphorus, available phosphorus, and available potassium content. Principal coordinate analysis (PCoA) indicated that strain VY-1 significantly influenced bacterial community composition, with Proteobacteria, Firmicutes, Chloroflexi, among others, being the main differential taxa. Redundancy analysis (RDA) revealed that available phosphorus, available potassium, and pH were the primary factors affecting bacterial communities. Partial Least Squares Discriminant Analysis (PLS-DA) demonstrated that strain VY-1 modulated the metabolite profile of Hybrid pennisetum rhizosphere soil, with 27 differential metabolites showing significant differences, including 19 up-regulated and eight down-regulated expressions. These differentially expressed metabolites were primarily involved in metabolism and environmental information processing, encompassing pathways such as glutamine and glutamate metabolism, α-linolenic acid metabolism, pyrimidine metabolism, and purine metabolism. This study utilized 16S rRNA high-throughput sequencing and metabolomics technology to investigate the impact of the plant growth-promoting bacterium Enterobacter sp. VY-1 on the growth and Cd enrichment of Hybrid pennisetum, providing insights into the regulatory role of plant growth-promoting bacteria in microbial community structure and metabolic function, thereby improving the microbiological mechanisms of phytoremediation.

Physiological tolerance of black locust (Robinia pseudoacacia L.) and changes of rhizospheric bacterial communities in response to Cd and Pb in the contaminated soil

Woody plants possess great potential for phytoremediation of heavy metal-contaminated soil. A pot trial was conducted to study growth, physiological response, and Cd and Pb uptake and distribution in black locust (Robinia pseudoacacia L.), as well as the rhizosphere bacterial communities in Cd and Pb co-contaminated soil. The results showed that R. pseudoacacia L. had strong physiological regulation ability in response to Cd and Pb stress in contaminated soil. The total chlorophyll, malondialdehyde (MDA), soluble protein, and sulfhydryl contents, as well as antioxidant enzymes (superoxide dismutase, peroxidase, catalase) activities in R. pseudoacacia L. leaves under the 40 mg·kg-1 Cd and 1000 mg·kg-1 Pb co-contaminated soil were slightly altered. Cd uptake in R. pseudoacacia L. roots and stems increased, while the Pb content in the shoots of R. pseudoacacia L. under the combined Cd and Pb treatments decreased in relative to that in the single Pb treatments. The bacterial α-diversity indices (e.g., Sobs, Shannon, Simpson, Ace, and Chao) of R. pseudoacacia L. rhizosphere soil under Cd and Pb stress were changed slightly relative to the CK treatment. However, Cd and Pb stress could significantly (p < 0.05) alter the rhizosphere soil microbial communities. According to heat map and LEfSe (Linear discriminant analysis Effect Size) analysis, Bacillus, Sphingomonas, Terrabacter, Roseiflexaceae, Paenibacillus, and Myxococcaceae at the genus level were notably (p < 0.05) accumulated in the Cd- and/or Pb-contaminated soil. Furthermore, the MDA content was notably (p < 0.05) negatively correlated with the relative abundances of Isosphaeraceae, Gaiellales, and Gemmatimonas. The total biomass of R. pseudoacacia L. was positively (p < 0.05) correlated with the relative abundances of Xanthobacteraceae and Vicinamibacreraceae. Network analysis showed that Cd and Pb combined stress might enhance the modularization of bacterial networks in the R. pseudoacacia L. rhizosphere soil. Thus, the assembly of the soil bacterial communities in R. pseudoacacia L. rhizosphere may improve the tolerance of plants in response to Cd and/or Pb stress.

The Salinity Survival Strategy of Chenopodium quinoa: Investigating Microbial Community Shifts and Nitrogen Cycling in Saline Soils

Quinoa is extensively cultivated for its nutritional value, and its exceptional capacity to endure elevated salt levels presents a promising resolution to the agricultural quandaries posed by salinity stress. However, limited research has been dedicated to elucidating the correlation between alterations in the salinity soil microbial community and nitrogen transformations. To scrutinize the underlying mechanisms behind quinoa's salt tolerance, we assessed the changes in microbial community structure and the abundance of nitrogen transformation genes across three distinct salinity thresholds (1 g·kg-1, 3 g·kg-1, and 6 g·kg-1) at two distinct time points (35 and 70 days). The results showed the positive effect of quinoa on the soil microbial community structure, including changes in key populations and its regulatory role in soil nitrogen cycling under salt stress. Choroflexi, Acidobacteriota, and Myxococcota were inhibited by increased salinity, while the relative abundance of Bacteroidota increased. Proteobacteria and Actinobacteria showed relatively stable abundances across time and salinity levels. Quinoa possesses the ability to synthesize or modify the composition of keystone species or promote the establishment of highly complex microbial networks (modularity index > 0.4) to cope with fluctuations in external salt stress environments. Furthermore, quinoa exhibited nitrogen (N) cycling by downregulating denitrification genes (nirS, nosZ), upregulating nitrification genes (Archaeal amoA (AOA), Bacterial amoA (AOB)), and stabilizing nitrogen fixation genes (nifH) to absorb nitrate-nitrogen (NO3-_N). This study paves the way for future research on regulating quinoa, promoting soil microbial communities, and nitrogen transformation in saline environments.

Effect of planting salt-tolerant legumes on coastal saline soil nutrient availability and microbial communities

Soil salinization is a serious global environmental problem affecting sustainable development of agriculture. Legumes are excellent candidates for the phytoremediation of saline soils; however, how soil microbes mediate the amelioration of coastal saline ecosystems is unknown. In this study, two salt-tolerant legumes, Glycine soja and Sesbania cannabina were planted in coastal saline soil for three years. Soil nutrient availability and microbiota structure (including bacteria, fungi, and diazotrophs) were compared between the phytoremediated soils and control soil (barren land). Planting legumes reduced soil salinity, and increased total carbon, total nitrogen, and NO3--N contents. Among the soil microbiota, some nitrogen-fixing bacteria (e.g., Azotobacter) were enriched in legumes, which were probably responsible for soil nitrogen accumulation. The complexity of the bacterial, fungal, and diazotrophic networks increased significantly from the control to the phytoremediated soils, suggesting that the soil microbial community formed closer ecological interactions during remediation. Furthermore, the dominant microbial functions were chemoheterotrophy (24.75%) and aerobic chemoheterotrophy (21.97%) involved in the carbon cycle, followed by nitrification (13.68%) and aerobic ammonia oxidation (13.34%) involved in the nitrogen cycle. Overall, our findings suggested that G. soja and S. cannabina legumes were suitable for ameliorating saline soils as they decreased soil salinity and increased soil nutrient content, with microorganisms especially nitrogen-fixing bacteria, playing an important role in this remediation process.

Recent Advances in Microbial-Assisted Remediation of Cadmium-Contaminated Soil

Soil contamination with cadmium (Cd) is a severe concern for the developing world due to its non-biodegradability and significant potential to damage the ecosystem and associated services. Industries such as mining, manufacturing, building, etc., rapidly produce a substantial amount of Cd, posing environmental risks. Cd toxicity in crop plants decreases nutrient and water uptake and translocation, increases oxidative damage, interferes with plant metabolism and inhibits plant morphology and physiology. However, various conventional physicochemical approaches are available to remove Cd from the soil, including chemical reduction, immobilization, stabilization and electro-remediation. Nevertheless, these processes are costly and unfriendly to the environment because they require much energy, skilled labor and hazardous chemicals. In contrasting, contaminated soils can be restored by using bioremediation techniques, which use plants alone and in association with different beneficial microbes as cutting-edge approaches. This review covers the bioremediation of soils contaminated with Cd in various new ways. The bioremediation capability of bacteria and fungi alone and in combination with plants are studied and analyzed. Microbes, including bacteria, fungi and algae, are reported to have a high tolerance for metals, having a 98% bioremediation capability. The internal structure of microorganisms, their cell surface characteristics and the surrounding environmental circumstances are all discussed concerning how microbes detoxify metals. Moreover, issues affecting the effectiveness of bioremediation are explored, along with potential difficulties, solutions and prospects.

Bioremediation of Heavy Metals by the Genus Bacillus

Environmental contamination with heavy metals is one of the major problems caused by human activity. Bioremediation is an effective and eco-friendly approach that can reduce heavy metal contamination in the environment. Bioremediation agents include bacteria of the genus Bacillus, among others. The best-described species in terms of the bioremediation potential of Bacillus spp. Are B. subtilis, B. cereus, or B. thuringiensis. This bacterial genus has several bioremediation strategies, including biosorption, extracellular polymeric substance (EPS)-mediated biosorption, bioaccumulation, or bioprecipitation. Due to the above-mentioned strategies, Bacillus spp. strains can reduce the amounts of metals such as lead, cadmium, mercury, chromium, arsenic or nickel in the environment. Moreover, strains of the genus Bacillus can also assist phytoremediation by stimulating plant growth and bioaccumulation of heavy metals in the soil. Therefore, Bacillus spp. is one of the best sustainable solutions for reducing heavy metals from various environments, especially soil.

Wastewater treatment effectiveness is facilitated by crucial bacterial communities in the wetland ecosystem

Microorganisms play essential roles in nutrient removal and biogeochemical cycling during wastewater treatment. However, little is known about the main roles of key functional bacterial communities in wastewater treatment processes. We collected 18 water samples and 15 sediment samples from the six operational subsystems of the constructed wetland, among which the contact oxidation pond, enhanced hybrid biofilm reactor, and central stabilization pond are the main wastewater treatment units in the constructed wetland, and then investigated the bacterial communities using 16S rRNA gene targeting and sequencing to address this knowledge gap. The results indicated that the composition of the bacterial community is closely related to the efficiency of pollutant removal. The abundant carbon metabolism function increased the removal of nitrate‑nitrogen (NO₃^--N) and total nitrogen (TN) by the contact oxidation pond by 89.84 % and 38.91 %, respectively. The overlap of ecological niches and the presence of pathogenic bacteria substantially affect effluent wastewater treatment. Second, NO₃^--N (p < 0.001) was the most important factor driving the bacterial community composition in water and sediments. Furthermore, the positive structure was prevalent in the cooccurrence network of water samples (87.24 %) and sediments (76.53 %) of the wetland, and this positive structure with keystone species was critical for the adaptation of the bacterial community to environmental filtration. In summary, this study reveals the distribution patterns of bacterial communities in different wastewater treatment processes and their driving factors and provides new perspectives on the link between the bacterial community composition and wastewater treatment.

Bama Pig Manure Organic Fertilizer Regulates the Watermelon Rhizosphere Bacterial Community to Inhibit the Occurrence of Fusarium Wilt Under Continuous Cropping Conditions

Fusarium wilt caused by Fusarium oxysporum f. sp. niveum is an important manifestation of continuous cropping barrier, which causes the quality and yield of watermelon to decline. In early stage of this study, the organic fertilizer fermented by Bama pig manure applied in soil was proved to significantly inhibit the occurrence of disease by improving the structure of soil microbial community. However, the mechanism was not clear. The high-throughput sequencing technology, combined with network and PICRUSt2 function analysis was used to investigate it. MiSeq sequencing showed that the bacterial community of organic fertilizer treated soil was composed of 34 phyla and 768 genera, the number of genera was higher than that of sterile water treated soil. Fertilization significantly increased the diversity and changed the composition of bacterial community based on alpha, beta diversity, and ANOSIM/Adonis analysis. LEfSe species difference and network analysis showed that fertilization improved the relative abundance of bacteria with biological control or plant growth promotion characteristics in soil, such as Sphingomonas, Halobacillus, Nocardioides, and enhanced the interaction between rhizosphere bacteria, made the network structure more complex. PICRUSt2 also revealed fertilization promoted the bacterial function, such as metabolism and genetic information processing. These results showed that the pig manure organic fertilizer might reduce the occurrence of Fusarium wilt by regulating bacterial community, interaction, and functional metabolism in watermelon rhizosphere soil.

Facilitation of Morus alba L. intercropped with Sedum alfredii H. and Arundo donax L. on soil contaminated with potentially toxic metals

Tree-herb intercropping is a prospective approach for the ecological remediation of soil contaminated with potentially toxic metals (PTMs). In this study, the facilitation and microbial community response of woody plant Morus alba L. intercropped with Cd/Zn hyperaccumulator Sedum alfredii H. and pioneer plant Arundo donax L. were carried out in the PTM-contaminated soil. The results indicated that the intercropping system can improve M. alba L. growth, as well as increase its PTMs uptake. The dried biomass of M. alba L. in the intercropping system was increased observably (p < 0.05) by 55.1%. Meanwhile, the contents of chlorophyll in M. alba L. leaves, PTMs contents in M. alba L. roots, and the relative abundance of Rhizobiaceae, Singulisphaera, Isosphaeraceae, and Arthrobacter in the M. alba L. rhizosphere were also notably (p < 0.05) enhanced. Meanwhile, the interactions of microorganisms in the intercropped plants rhizosphere might contribute to improving the biological quality of the contaminated soil. Soil sucrase and acid phosphatase activities in the intercropping system were significantly (p < 0.05) increased by 97.03% and 34.91% relative to the control. Furthermore, in the intercropping system, 93.61%, 61.30%, and 79.18% of Cd, Pb, and Zn were extracted by S. alfredii H., 72.16% of Cu was extracted by A. donax L., and 46.38% of Mn was extracted by M. alba L., which indicated that the extraction amounts of PTMs among the intercropped plants were relatively compensated. The results suggested that the tree-herb intercropping might increase the coexistence of plants and facilitate the adaptability for ecological remediation of PTM-contaminated soils.

Pseudomonas sp. TCd-1 significantly alters the rhizosphere bacterial community of rice in Cd contaminated paddy field

Cadmium (Cd) pollution of paddy soils is one of the main concerns causing food security and environmental problems. Microbial bioremediation is an effective and eco-friendly measure that uses microbes to reduce Cd accumulation in crops. Additionally, rhizosphere bacterial communities also act essential roles in crop tolerance of heavy metals. However, the effects of inoculations with Cd resistant bacteria on crop rhizosphere bacterial communities under Cd exposure are largely unknown. In this study, we used high-throughput 16S rRNA gene sequencing technologies to explore the community structure and co-occurrence network of the rhizosphere bacterial communities associated with the rice crop under different Cd treatments and the application of Cd-tolerant strain Pseudomonas sp. TCd-1. We found that the strain TCd-1 both significantly reduced the rhizobacterial alpha diversity and changed the beta diversity. PERMANOVA and NMDS analysis showed that Cd stress and TCd-1 strain could act as strong environmental filters resulting in observable differentiation of rhizobacterial community composition among different groups. In addition, RDA results indicated that the rhizosphere pH, root Cd content, catalase (CAT), urease (URE), gibberellic acid (GA3) exert significant association with rhizosphere bacterial assembly. PICRUSt analysis revealed that the TCd-1 strain improved the metabolic capacity of rhizosphere bacteria under Cd stress. Furthermore, co-occurrence network topological features and keystone taxa also varied among different groups. This study could provide necessary insights into developing an efficient bioremediation and safe production of rice crops in Cd contaminated paddy fields with the application of Pseudomonas sp. TCd-1 strain, as well as advance our understanding of the principles of rhizosphere bacterial community assembly under Cd stress.

Phytoremediation of cadmium-contaminated sediment using Hydrilla verticillata and Elodea canadensis harbor two same keystone rhizobacteria Pedosphaeraceae and Parasegetibacter

Aquatic macrophytes have been widely employed for in-situ phytoremediation of cadmium (Cd) polluted sediments. But, little is known about the responses of rhizosphere bacteria and their interspecific interactions to phytoremediation. In this study, the α-diversity, community composition, co-occurrence network and keystone species of sediment bacteria in rhizosphere zones of two typical macrophytes, Hydrilla verticillata and Elodea canadensis, were investigated using 16S rRNA gene high-throughput sequencing. The results showed that after fifty days of phytoremediation, a group of specialized sediment bacteria were assembled in the rhizosphere zones closely associated with different host macrophytes. Rhizosphere micro-environments, i.e., the increases of redox potential and organic matter and the decreases of pH, nitrogen and phosphorus, reduced bacterial α-diversity through niche-based species-sorting process, which in turn reduced interspecific mutualistic relationships. But meanwhile, benefiting from the nutrients supplied from macrophyte roots, more bacterial species survived in the highly Cd-contaminated sediments (50 mg kg^-1). In addition, the co-occurrence network revealed that both macrophytes harbored two same keystone bacteria with the high betweenness centrality values, including the family Pedosphaeraceae (genus_unclassified) and genus Parasegetibacter. Their relative abundances were up to 28-fold and 25-fold higher than other keystone species, respectively. Furthermore, these two keystone bacteria were metabolic generalists with vital ecological functions, which posed significant potentials for promoting plant growth and tolerating Cd bio-toxicity. Therefore, the identified keystone rhizobacteria, Pedosphaeraceae and Parasegetibacter, would be potential microbial modulations applied for the future optimization of phytoremediation in Cd-contaminated sediment.

Cadmium-tolerant bacteria: current trends and applications in agriculture

Cadmium (Cd) is considered a toxic heavy metal; nevertheless, its toxicity fluctuates for different organisms. Cadmium-tolerant bacteria (CdtB) are diverse and non-phylogenetically related. Because of their ecological importance these bacteria become particularly relevant when pollution occurs and where human health is impacted. The aim of this review is to show the significance, culturable diversity, metabolic detoxification mechanisms of CdtB and their current uses in several bioremediation processes applied to agricultural soils. Further discussion addressed the technological devices and the possible advantages of genetically modified CdtB for diagnostic purposes in the future.

Interactions between pyrene and heavy metals and their fates in a soil-maize (Zea mays L.) system: Perspectives from the root physiological functions and rhizosphere microbial community

The co-occurrence of polycyclic aromatic hydrocarbons (PAHs) and heavy metals in agricultural soils has become a worldwide food crop security concern. Pot experiments, rhizosphere microbial metagenomic sequencing, and root metatranscriptomic sequencing were performed to investigate the interactions among pyrene, Cu, and Cd in a soil-maize (Zea mays L.) system. This study provided direct evidence that the co-presence of PAHs and heavy metals changed the root physiological functions and the rhizosphere microbial community, which subsequently influenced the fate of the contaminants. Co-contamination at low levels tended to enhance the uptake potential and biodegradation performance of the plant, whereas increased contaminant concentrations produced opposite effects. The co-presence of 1000 mg/kg Cu decreased the abundance of Mycobacterium in the rhizosphere and reduced pyrene degradation by 12%-16%. The presence of 400-750 mg/kg pyrene altered the metabolic processes, molecular binding functions, and catalytic activity of enzymes in the maize roots, thus impeding the phytoextraction of Cu and Cd. Competitive absorption between Cu and Cd was observed for the 800-1000 mg/kg Cu and 50-100 mg/kg Cd co-treatment, in which Cu showed a competitive advantage, enhancing its root-to-shoot translocation. These findings provide important information for the production of safe crops and for the development of phytoremediation technologies.

Responses of rhizosphere bacterial communities, their functions and their network interactions to Cd stress under phytostabilization by Miscanthus spp

Miscanthus has good tolerance to heavy metals (HMs) and has received increasing attention in studies of HM-contaminated soil remediation. In this study, four Miscanthus cultivars (M. lutarioriparius Xiangnadi NO4, M. sinensis Xiangmang NO1, M. lutarioriparius × M. sinensis hybrid Xiangzamang NO1, and M. floridulus Wujiemang NO1) that grow in China were studied. Their tolerance and enrichment abilities in soils containing 50 mg kg^-1 cadmium (Cd) and the structure and function of their rhizosphere bacterial communities during the remediation process were analyzed. The results exhibiting a tolerance index (TI) higher than 75 in roots and the aboveground parts (TI > 60, indicating highly tolerant plants) indicated that all four Miscanthus cultivars were tolerant to high Cd concentrations. Moreover, Cd was mainly enriched in roots, the translocation ability from roots to aboveground parts was weak, and the four cultivars exhibited phytostabilization ability in Cd-contaminated soils. High-throughput sequencing (HTS) analysis showed that the Miscanthus rhizosphere bacterial community comprised 33 phyla and 446 genera, including plant growth-promoting rhizobacteria (PGPRs), such as Bacillus, Sphingomonas, and Mesorhizobium. The addition of Cd affected the Miscanthus rhizosphere bacterial community and reduced community diversity. Phylogenetic molecular ecological networks (pMENs) indicated that Cd addition reduced interactions between Miscanthus rhizosphere bacteria and thereby led to a simpler network structure, increased the number of negative-correlation links, enhanced the competition between rhizosphere bacterial species, reduced the number of key bacteria, and changed the composition of those bacteria. PICRUSt functional predictive analysis indicated that Cd stress reduced soil bacterial functions in the Miscanthus rhizosphere. The results of this study provide a basis for the remediation of Cd-contaminated soils by Miscanthus and provide a reference for the subsequent regulation of Miscanthus remediation efficiency by PGPRs or key bacteria.

Metagenomic Insight into the Community Structure of Maize-Rhizosphere Bacteria as Predicted by Different Environmental Factors and Their Functioning within Plant Proximity

The rhizosphere microbiota contributes immensely to nutrient sequestration, productivity and plant growth. Several studies have suggested that environmental factors and high nutrient composition of plant's rhizosphere influence the structural diversity of proximal microorganisms. To verify this assertion, we compare the functional diversity of bacteria in maize rhizosphere and bulk soils using shotgun metagenomics and assess the influence of measured environmental variables on bacterial diversity. Our study showed that the bacterial community associated with each sampling site was distinct, with high community members shared among the samples. The bacterial community was dominated by Proteobacteria, Actinobacteria, Acidobacteria, Gemmatimonadetes, Bacteroidetes and Verrucomicrobia. In comparison, genera such as Gemmatimonas, Streptomyces, Conexibacter, Burkholderia, Bacillus, Gemmata, Mesorhizobium, Pseudomonas and Micromonospora were significantly (p ≤ 0.05) high in the rhizosphere soils compared to bulk soils. Diversity indices showed that the bacterial composition was significantly different across the sites. The forward selection of environmental factors predicted N-NO₃ (p = 0.019) as the most influential factor controlling the variation in the bacterial community structure, while other factors such as pH (p = 1.00) and sulfate (p = 0.50) contributed insignificantly to the community structure of bacteria. Functional assessment of the sampling sites, considering important pathways viz. nitrogen metabolism, phosphorus metabolism, stress responses, and iron acquisition and metabolism could be represented as Ls > Rs > Rc > Lc. This revealed that functional hits are higher in the rhizosphere soil than their controls. Taken together, inference from this study shows that the sampling sites are hotspots for biotechnologically important microorganisms.

Microbial communities in the rhizosphere of different willow genotypes affect phytoremediation potential in Cd contaminated soil

Plant-associated microorganisms play an important role in controlling heavy metal uptake and accumulation in aerial parts. The microbial community and its interaction with Cd accumulation by willow were assessed to explore the association of phytoextraction efficiency and rhizospheric microbial populations. Therefore, the rhizosphere microbial compositions of three willow genotypes grown in two Cd polluted sites were investigated, focusing on their interactions with phytoremediation potential. Principal coordinate analysis revealed a significant effect of genotype on the rhizosphere microbial communities. Distinct beneficial microorganisms, such as plant growth promoting bacteria (PGPB) and mycorrhizal fungi, were assembled in the rhizosphere of different willow genotypes. Linear mixed models showed that the relative abundance of PGPB was positively associated (p < 0.01) with Cd accumulation, since these microbes significantly increased willow growth. The higher abundance of arbuscular mycorrhizal fungi in the rhizosphere of Salix × aureo-pendula CL 'J1011' at the Kejing site, showed a negative correlation with the Cd content, but a positive correlation with biomass. Conversely, mycorrhizal fungi, were more abundant in the rhizosphere of S. × jiangsuensis CL. 'J2345' and positively correlated with the Cd content in willow tissues. This study provides new insights into the distinctive microbial communities in rhizosphere of different willow genotypes, which may be consistent with the phytoremediation potential.

Computational Biology and Machine Learning Approaches to Understand Mechanistic Microbiome-Host Interactions

The microbiome, by virtue of its interactions with the host, is implicated in various host functions including its influence on nutrition and homeostasis. Many chronic diseases such as diabetes, cancer, inflammatory bowel diseases are characterized by a disruption of microbial communities in at least one biological niche/organ system. Various molecular mechanisms between microbial and host components such as proteins, RNAs, metabolites have recently been identified, thus filling many gaps in our understanding of how the microbiome modulates host processes. Concurrently, high-throughput technologies have enabled the profiling of heterogeneous datasets capturing community level changes in the microbiome as well as the host responses. However, due to limitations in parallel sampling and analytical procedures, big gaps still exist in terms of how the microbiome mechanistically influences host functions at a system and community level. In the past decade, computational biology and machine learning methodologies have been developed with the aim of filling the existing gaps. Due to the agnostic nature of the tools, they have been applied in diverse disease contexts to analyze and infer the interactions between the microbiome and host molecular components. Some of these approaches allow the identification and analysis of affected downstream host processes. Most of the tools statistically or mechanistically integrate different types of -omic and meta -omic datasets followed by functional/biological interpretation. In this review, we provide an overview of the landscape of computational approaches for investigating mechanistic interactions between individual microbes/microbiome and the host and the opportunities for basic and clinical research. These could include but are not limited to the development of activity- and mechanism-based biomarkers, uncovering mechanisms for therapeutic interventions and generating integrated signatures to stratify patients.

Bio-remediation approaches for alleviation of cadmium contamination in natural resources

Cadmium (Cd) is a harmful heavy metal that can cause potent environmental and health hazards at different trophic levels through food chain. Cd is relatively non-biodegradable and persists for a long time in the environment. Considering the potential toxicity and non-biodegradability of Cd in the environment as well as its health hazards, this is an urgent issue of international concern that needs to be addressed by implicating suitable remedial approaches. The current article specifically attempts to review the different biological approaches for remediation of Cd contamination in natural resources. Further, bioremediation mechanisms of Cd by microbes such as bacteria, fungi, algae are comprehensively discussed. Studies indicate that heavy metal resistant microbes can be used as suitable biosorbents for the removal of Cd (up to 90%) in the natural resources. Soil-to-plant transfer coefficient (TC) of Cd ranges from 3.9 to 3340 depending on the availability of metal to plants and also on the type of plant species. The potential phytoremediation strategies for Cd removal and the key factors influencing bioremediation process are also emphasized. Studies on molecular mechanisms of transgenic plants for Cd bioremediation show immense potential for enhancing Cd phytoremediation efficiency. Thus, it is suggested that nano-technological based integrated bioremediation approaches could be a potential futuristic path for Cd decontamination in natural resources. This review would be highly useful for the biologists, chemists, biotechnologists and environmentalists to understand the long-term impacts of Cd on ecology and human health so that potential remedial measures could be taken in advance.

Strong linkages between dissolved organic matter and the aquatic bacterial community in an urban river

Aquatic bacterial communities play an important role in biogeochemical cycling in river ecosystems; however, knowledge of the linkages between bacterial communities and dissolved organic matter (DOM) in urban rivers is limited. Here, 16S rRNA amplicon sequencing and parallel factor (PARAFAC) modeling of excitation-emission fluorescence spectroscopy were used to analyze the compositions, co-occurrence patterns, and interactions with chromophoric DOM (CDOM) of bacterial communities in urban river water samples influenced by different human activities. The results revealed that two protein-like components accounted for 65.2 ± 9.56% of the total variability in all three fluorescence components, which suggests that CDOM in urban rivers is mainly a microbial source. In addition to pH and DO, CDOM is also an important factor affecting bacterial community structure, and the main classes (Gammaproteobacteria and Clostridia) and genera (Limnohabitans and Alpinimonas) showed strong positive correlations with terrestrial humic-like C1 and tryptophan-like C2, respectively. When autotrophic and heterotrophic bacteria coexist in urban rivers, the production and degradation of CDOM will occur simultaneously. Furthermore, the riverine bacterial co-occurrence network had a nonrandom modular structure, which was mainly driven by classification correlation and bacterial function. The high abundance of genes related to xenobiotic metabolism, carbon metabolism and nitrogen metabolism in the urban river indicated that anthropogenic activity may be the dominant selective force altering the bacterial communities. Overall, our results provide a novel view for the assembly of bacterial communities in urban river ecosystems under the influence of different human activities.

Microbial network succession along a current gradient in a bio-electrochemical system

A lab-scale three dimensional biofilm-electrode reactor (3DBER) coupled with sulfur/iron (3DBER-Fe/S) system was established to examine the impacts of current gradient on the performances and microbial network dynamics. Results showed that generally low current could promote nitrogen and phosphorus removal, while high current caused the inhibition of nutrients removal. Molecular ecological network (MEN) analysis showed that the current altered the overall architecture of the networks, and low currents could improve the scale and complexity of networks (<100 mA), while high current (≥100 mA) likely decrease the networks scale and complexity. Stronger competition was observed among Proteobacteria and Chloroflexi at high current conditions, which may be relevant to the deterioration of nutrients removal. In addition, the current dramatically altered the network interactions among denitrifiers, and the keystone species were intensively dynamic among various networks under the current gradient.

Contribution of influent rivers affected by different types of pollution to the changes of benthic microbial community structure in a large lake

As a microbial group in watershed ecosystems, the bacterial community is a sensitive indicator of external environmental fluctuations. However, the effects of different sources of exogenous pollution on the diversity and structure of bacterial communities in inflow rivers and lakes have not been studied in depth. In this study, we used 16S rRNA gene sequencing technology to study the diversity and composition of bacterial communities in rivers affected by different types of pollution. The results showed that the composition of the bacterial communities in rivers with different exogenous pollution sources was different. For example, the genus Arenimonas, which belongs to the Gamma-proteobacteria, is extensively enriched in IDPR (industrially and domestically polluted rivers) and ADPR (agriculturally and domestically polluted rivers) (KW, p < 0.05), while the genus Micromonospora is a more unique genus found in APR (agriculturally polluted rivers). When exploring the topology and classification characteristics of river microbial symbiosis models, it was found that the bacterial community symbiosis network is divided into six modules under different exogenous pollution regimes, and the nodes in the different modules perform different functions, such as the IDPR-dominated module I. In the network, the relatively abundant the genus Flavobacterium and the genus Nitrospira are the key factors driving the nitrogen cycle in the watershed where the samples were collected. In addition, our research indicates that communities in lake environments may be more susceptible to disturbances of various physiological or functional redundancies, thus retaining their original community structure. Overall, this study emphasizes that adaptive changes in the bacterial community structure of the sediments in the catchment and the occurrence of interactions are responses to different exogenous pollution sources.

Plant growth promotion and enhanced uptake of Cd by combinatorial application of Bacillus pumilus and EDTA on Zea mays L

In developing countries, Cd contamination is ubiquitous which limits agriculture productivity. The current study was designed to investigate the efficacy of plant-Bacillus pumilus-ethylene diamine tetraacetic acid (EDTA) and plant-microbe-chelator (PMC) synergy for enhanced plant growth and Cd-uptake potential of Zea mays in industrially contaminated and cadmium (Cd) spiked soil. A pot experiment was conducted by growing Z. mays seedlings either inoculated with B. pumilus or un-inoculated along with the application of 5 mM EDTA. Plants were exposed to two levels of Cd contamination for 45 days. An increase in Cd uptake was observed in Z. mays inoculated with B. pumilus followed by EDTA treatment as compared to non-inoculated and un-treated ones. Zea mays showed improved values with PMC approach for different growth parameters including root length (41%), shoot length (40%), fresh weight (59%), dry weight (49%), chlorophyll contents (49%), and relative water contents (30%). Higher tolerance index (117%) was observed for plants grown in soil spiked with 300 mg kg^-1 Cd (S2). PMC application markedly enhanced Cd uptake potential of Z. mays up to 12% and 68.8%, respectively, in S1 and S2 soil. While the PMC application increased Cd accumulation capacity of Z. mays by 71.2% and 52.5% in S1 and S2 soil. The calculated bioaccumulation and translocation factor revealed that Z. mays possess Cd uptake potential, and this ability can be significantly enhanced with PMC application.

Linking bacterial community shifts with changes in the dissolved organic matter pool in a eutrophic lake

Aquatic bacterial communities play crucial roles in the circulation of nutrients in watershed ecosystems. However, the interaction between bacterial communities and chromophoric dissolved organic matter (CDOM) in freshwater ecosystems has not been studied in depth. In our study, we examined the constitution and interactions of CDOM with the bacterial community in Lake Chaohu and its inflow rivers under the influence of different exogenous pollutants. The results revealed that the bacterial community diversity in the inflow rivers was significantly lower than that in the lake sites. Clustering of different types of polluted inflow rivers integrated with the most abundant genera observed in specific areas indicated that environmentally guided species selection had a large impact on the composition of aquatic bacterial communities. Moreover, our study suggests that communities in lake environments may be more susceptible to interference through a variety of physiologies or via functional redundancy, allowing them to preserve their community structure. Through linear discriminant analysis effect size (Lefse) methods, we revealed that some taxa (from phylum to genus) were consistently enriched in the lake sites. Based on correlation network analysis results, the supersession niches of bacterial community members related to different CDOM in the biogeochemical process was determined. This study provides an ecological basis for the control of external pollution and the protection of the water environment in watershed ecosystems.

Response of rhizospheric and endophytic bacterial communities of white mustard (Sinapis alba) to bioaugmentation of soil with the Pseudomonas sp. H15 strain

A factor that may significantly increase the efficacy of phytoextraction is soil bioaugmentation with specific bacteria, which can alter the composition of rhizospheric and endophytic bacterial communities. The aim of this study was to compare the effect of soil treatment with living (bioaugmentation) and dead (control) cells of the plant growth-promoting metal-resistant endophytic strain Pseudomonas sp. H15 on the bacterial community composition in the rhizo- and endo-sphere of white mustard during enhanced phytoextraction. The bacterial communities in the rhizosphere were dominated (51.7-68.2%) by Proteobacteria, regardless of the soil treatment or sampling point. A temporary increase in the number of sequences belonging to Gammaproteobacteria (up to 37.3%) was only observed 24 h after the soil treatment with living Pseudomonas sp. H15 cells, whereas for the remaining samples, the relative abundance of this class did not exceed 7.1%. The relative abundance of Proteobacteria in the endosphere of the roots, stems, and leaves of white mustard was higher in the control than in bioaugmented plants. The most pronounced dominance of the Gammaproteobacteria sequences was observed in the stems and leaves of the control plants at the first sampling point, which strongly indicates the ability of the plants to rapidly uptake DNA from soil and translocate it to the aboveground parts of the plants. Additionally, the bioaugmentation of the soil caused a diverse shift in the bacterial communities in the rhizo- and endo-sphere of white mustard compared to control. The most distinct differences, which were dependent on the treatment, were observed in the endosphere of plants at the beginning of the experiment and decreased over time. These results indicate that the rhizo- and endo-biome of white mustard reacts to soil bioaugmentation and may influence the efficiency of bacterial-assisted phytoextraction.

Microbial communities respond to microenvironments in lungs of mice under simulated exposure to cadmium aerosols

Inhalable pollutants are inducing factors of lung diseases and have been widely studied. Previous studies described imbalances in pulmonary microbial communities and representatively predominant microorganisms in clinical specimens of individuals with lung diseases. However, the direct effect of inhalable pollutants on pulmonary microorganisms has not been determined to date. Cadmium is a common inhalable pollutant from manufacturing activities, and its effect on pulmonary microorganisms was investigated in this study. Such techniques as optical respiratory plethysmography, high-throughput pulmonary histological assessment and differential centrifugation were used to characterize pulmonary microenvironments, and high-throughput sequencing was used to analyze pulmonary microbial diversity. We found variations in pulmonary microenvironmental factors, such as air supply level, nutrition and inflammatory stress. Under inhalable cadmium exposure at different doses, pulmonary microorganisms were differentially subjected and sensitive to various microenvironmental stresses (e.g., inflammation, pH, ventilation, nutrition and related changes of lung tissue structure) and might participate in microenvironmental remodeling, such as pneumonia and pulmonary fibrosis. Inflammatory stress and Lactobacillus were the main microenvironmental factor and susceptible microorganism, respectively. The various pulmonary microenvironments influenced the metabolisms of pulmonary microbial communities, presenting differences in microbial collinearities, gene function levels and metabolic pathway levels among groups.

Rhizosphere Bacterial Community Structure and Predicted Functional Analysis in the Water-Level Fluctuation Zone of the Danjiangkou Reservoir in China During the Dry Period

The water-level fluctuation zone (WLFZ) is a transitional zone between terrestrial and aquatic ecosystems. Plant communities that are constructed artificially in the WLFZ can absorb and retain nutrients such as nitrogen (N) and phosphorus (P). However, the microbial community composition and function associated with this process have not been elucidated. In this study, four artificially constructed plant communities, including those of herbs (Cynodon dactylon and Chrysopogon zizanioides), trees (Metasequoia glyptostroboides), and shrubs (Salix matsudana) from the newly formed WLFZ of the Danjiangkou Reservoir were evaluated. The bacterial community compositions were analyzed by 16S rRNA gene sequencing using a MiSeq platform, and the functions of these communities were assessed via Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis. The results showed that the bacterial communities primarily comprised 362 genera from 24 phyla, such as Proteobacteria, Acidobacteria, Actinobacteria, and Gemmatimonadetes, showing the richness of the community composition. Planting altered the bacterial community composition, with varying effects observed among the different plant types. The bacterial community functional analysis revealed that these bacteria were primarily associated with six biological metabolic pathway categories (e.g., metabolism, genetic information processing, and environmental information processing) with 34 subfunctions, showing the richness of community functions. The planting of M. glyptostroboides, S. matsudana, and C. dactylon improved the metabolic capabilities of bacterial communities. N- and P-cycling gene analysis showed that planting altered the N- and P-cycling metabolic capacities of soil bacteria. The overall N- and P-metabolic capacity was highly similar between C. dactylon and C. zizanioides samples and between S. matsudana and M. glyptostroboides samples. The results of this study provide a preliminary analysis of soil bacterial community structure and function in the WLFZ of the Danjiangkou Reservoir and provides a reference for vegetation construction in this zone.

Physiological responses of Morus alba L. in heavy metal(loid)-contaminated soil and its associated improvement of the microbial diversity

Woody plants have considerable application potential in the phytoremediation schemes, owing to their long-lived large biomass and prosperous root systems in heavy metal(loid)-contaminated soil. Under greenhouse conditions, the physiological response characteristics and phytoremediation possibility of Morus alba L. and its associated improvement of the bacterial and arbuscular mycorrhizal fungal (AMF) diversities in heavy metal(loid) co-contaminated soils were investigated. The results showed that the cultivated M. alba L. plant exhibited significant tolerance against the heavy metal(loid)s in co-contaminated soil and that the microbial diversities were improved notably. The contents of malondialdehyde (MDA) in M. alba L. leaves decreased with cultivation from 90 to 270 days, while the superoxide dismutase, peroxidase and catalase activities were maintained at normal levels to eliminate the production of lipid peroxides. The chemical compositions (e.g. amino acids, carbohydrates and proteins) in the root of M. alba L. fluctuated slightly throughout the cultivation period. Meanwhile, Cd, Pb and Zn were majorly concentrated in the M. alba L. roots, and the maximum contents were 23.4, 7.40 and 615.5 mg/kg, respectively. According to the polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis results, the influence of M. alba L. on the rhizosphere AMF community was greater than that on the bacteria community. Meanwhile, the bacterial and AMF Shannon diversity indexes in the contaminated soil were enhanced by 18.7-22.0% and 7.14-16.4%, respectively, with the presence of M. alba L. Furthermore, the correlations between the availability of As, Cd, Pb, and Zn and Shannon diversity indexes of the bacterial and AMF communities were significantly (p < 0.05) positive with the phytoremediation of M. alba L. Therefore, M. alba L. can be suggested as a potential plant candidate for ecological remediation and for simultaneously improving the activity and diversity of microorganisms in contaminated soils.

Illumina MiSeq sequencing and network analysis the distribution and co-occurrence of bacterioplankton in Danjiangkou Reservoir, China

Network analysis has contributed to studies of the interactions of microorganisms and the identification of key populations. However, such analysis has rarely been conducted in the study of reservoir bacterioplankton communities. This study investigated the bacterioplankton community composition in the surface water of the Danjiangkou Reservoir using the Illumina MiSeq sequencing platform. We observed that the bacterioplankton community primarily consisted of 27 phyla and 336 genera, including Actinobacteria, Proteobacteria, and Bacteroidetes, demonstrating the richness of the community composition. Redundancy analysis of the bacterioplankton communities and environmental variables showed that the total nitrogen (TN), pH, chemical oxygen demand (COD), and permanganate index (COD_Mn) were important factors affecting the bacterioplankton distribution. Network analysis was performed using the relative abundances of bacterioplankton based on the phylogenetic molecular ecological network (pMEN) method. The connectivity of node i within modules (Zi), the connectivity of node i among modules (Pi), and the number of key bacteria were high at the Taizishan and Heijizui sites, which were associated with higher TN contents than at the other sites. Among the physicochemical properties of water, TN, ammonia nitrogen (NH₄-N), pH, COD, and dissolved oxygen (DO) might have great influences on the functional units of the bacterial communities in bacterioplankton molecular networks. This study improves the understanding of the structure and function of bacterioplankton communities in the Danjiangkou Reservoir.

Habitat filtering shapes the differential structure of microbial communities in the Xilingol grassland

The spatial variability of microorganisms in grasslands can provide important insights regarding the biogeographic patterns of microbial communities. However, information regarding the degree of overlap and partitions of microbial communities across different habitats in grasslands is limited. This study investigated the microbial communities in three distinct habitats from Xilingol steppe grassland, i.e. animal excrement, phyllosphere, and soil samples, by Illumina MiSeq sequencing. All microbial community structures, i.e. for bacteria, archaea, and fungi, were significantly distinguished according to habitat. A high number of unique microorganisms but few coexisting microorganisms were detected, suggesting that the structure of microbial communities was mainly regulated by species selection and niche differentiation. However, the sequences of those limited coexisting microorganisms among the three different habitats accounted for over 60% of the total sequences, indicating their ability to adapt to variable environments. In addition, the biotic interactions among microorganisms based on a co-occurrence network analysis highlighted the importance of Microvirga, Blastococcus, RB41, Nitrospira, and four norank members of bacteria in connecting the different microbiomes. Collectively, the microbial communities in the Xilingol steppe grassland presented strong habitat preferences with a certain degree of dispersal and colonization potential to new habitats along the animal excrement- phyllosphere-soil gradient. This study provides the first detailed comparison of microbial communities in different habitats in a single grassland, and offers new insights into the biogeographic patterns of the microbial assemblages in grasslands.

Plant and microalgae consortium for an enhanced biodegradation of sulfamethazine

Pharmaceutical contamination in diverse water resources has been recognized as an emerging concern in environment because of its wide distribution and adverse effects on aquatic microorganisms and human health. Plant remediation with augmentation of microorganisms is a cost-effective and environmentally friendly approach toward an efficient treatment of pollutants, which can be easily applied in situ. (Bio)degradation of sulfamethazine (SMZ) by Iris pseudacorus, microalgal consortium, and plant-microalgal consortium was investigated. I. pseudacorus and microalgae could remove 63.5, and 25.8% of 1 mg SMZ L^-1, respectively, whereas, the plant-microalgal consortium achieved 74% removal. The identified intermediates extracted after plant remediation indicated (bio)degradation of SMZ was through ring cleavage, hydroxylation, and dehydroxylation. Pigment content (total chlorophyll and carotenoid) of I. pseudacorus was significantly influenced by SMZ stress. A phytoreactor (20 L) constructed with I. pseudacorus achieved 30.0% and 71.3% removal of 1 mg SMZ L^-1 from tap water and nutrient medium. This study has provided a better understanding of the metabolic mechanisms of SMZ in plants and showed the potential development of a plant-microalgal consortium as an advanced technology for treatment of these emerging contaminants. Graphical abstract.

Composition of bacterial communities in municipal wastewater treatment plant

Efforts to understand the environmental and biological factors that influence the dynamics of microbial communities have received substantial attention in microbial ecology. In this study, Illumina MiSeq high-throughput sequencing technology was used to examine the microbial community structure of activated sludge in municipal wastewater treatment systems (Chuzhou city, China). Overall, Proteobacteria, Chloroflexi, Actinobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, and Firmicutes were the most dominant phyla in the five activated sludge samples. However, the community structure of nitrifying bacteria was relatively simple, and diversity was low; only AOB (Nitrosomonas) and NOB (Nitrospira) were detected. The dominant bacteria in the anaerobic sludge, anoxic sludge and oxic sludge were the same, and each bacterial species was relatively uniform, with differences only in proportions. Redundancy analysis indicated that pH, TP and COD were strong environmental factors influencing the bacterial community distribution. PICRUSt was used to describe the metabolic and functional abilities of the activated sludge bacterial communities. The results emphasized the vast genetic diversity of these organisms, which are involved in various essential processes such as amino acid transport and metabolism, energy production and conversion, cell wall/membrane/envelope/biogenesis, signal transduction mechanisms, and carbohydrate transport and metabolism. Activated sludge of municipal wastewater treatment systems can be ranked in the following order based on the 16S rRNA gene copy numbers of the detected phylotypes: S1 > S2 > S4 > S5 > S3. This study provides basic data and a theoretical analysis of the optimal design and operation in wastewater treatment plants.

Effects of Plant Growth-Promoting Bacteria (PGPB) Inoculation on the Growth, Antioxidant Activity, Cu Uptake, and Bacterial Community Structure of Rape (Brassica napus L.) Grown in Cu-Contaminated Agricultural Soil

Previous analyses of plant growth-promoting bacteria (PGPB) combined with the remediation of heavy metal pollution in soil have largely been performed under potting or greenhouse conditions, and in situ remediation experiments under field conditions have rarely been reported. In this study, the effects of the metal-resistant PGPB Microbacterium oxydans JYC17, Pseudomonas thivervalensis Y1-3-9, and Burkholderia cepacia J62 on soil Cu pollution under rape remediation were studied in the farmland surrounding the Nanjing Jiuhuashan copper mining region in China. Following inoculation treatment for 50 days, the biomasses of the rape inoculated with strains JYC17, Y1-3-9, and J62 increased, and the total amounts of Cu uptake increased by 113.38, 66.26, and 67.91%, respectively, the translocation factor (TF) of rape inoculated with J62 was 0.85, a significant increase of 70.68%, thus improving the Cu remediation efficiency of the rape. Y1-3-9 and J62 affected the bioavailability of Cu in the soil, and the water-soluble Cu contents were increased by 10.13 and 41.77%, respectively, compared with the control. The antioxidant activities in the rape leaves showed that the tested bacteria increased the contents of antioxidant non-enzymatic substances, including ascorbic acid (ASA) and glutathione (GSH), which were increased by 40.24-91.22% and 9.89-17.67%, respectively, thereby reducing the oxidative stress caused by heavy metals and the contents of thiobarbituric acid-reactive substances (TBARS) and peroxidase (POD). PCR-denaturing gradient gel electrophoresis (PCR-DGGE) was used to analyze the effects of the tested bacteria on the cultivation-dependent and cultivation-independent bacterial communities in the root endosphere and rhizosphere soil of the rape. The sequencing results of the DGGE bands indicated that the tested bacteria colonized the endosphere and rhizosphere, and they became an important component of the cultivation-dependent bacteria. The canonical correspondence analysis (CCA) of the DGGE profile and similarity cluster analysis showed that the tested bacteria affected the cultivation-dependent and cultivation-independent bacterial communities in the root endosphere and rhizosphere. In this experiment, the effects and mechanisms of the combined plant-microbe remediation under field conditions were preliminarily studied, and the results are expected to provide a theoretical basis for future combined remediation experiments.

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

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

Intercropping with sunflower and inoculation with arbuscular mycorrhizal fungi promotes growth of garlic chive in metal-contaminated soil at a WEEE-recycling site

Heavy metal (HM) pollution in agricultural soils due to the recycling of waste electrical and electronic equipment (WEEE) has become a serious concern, but most farmers cannot afford the economic losses of fallow land during remediation. Thus, it is imperative to produce low-HM crops while remediating the contaminated soils. A 17-week pot experiment was conducted to investigate the growth and HM (Cd, Cu, Pb, Cr, Zn, and Ni) acquisition of garlic chives (Allium tuberosum Rottl. ex Spreng.) intercropped with sunflower (Helianthus annuus L.) and inoculated with (I_+M) or without (I_-M) the arbuscular mycorrhizal (AM) fungus Funneliformis caledonium on a severely HM-contaminated soil that was collected from a WEEE-recycling site. Compared with the monoculture control, the I_-M treatment significantly (P < 0.05) decreased Cd, Cu, Cr, Zn, and Ni concentrations in the shoots of chives through rhizosphere competition and HM (except Cr) transfer from the root to the shoot of chives, and increased the average shoot fresh weight (i.e., yield) of chives by 794% by alleviating HM toxicity. Compared with the I_-M treatment_, the I_+M treatment significantly increased soil phosphatase activity as well as root mycorrhizal colonization of both sunflower and chives. The I_+M treatment had no effect on the tissue P concentration of sunflower but elevated the average dry biomass (shoot plus root) and P acquisition level of sunflower by 179% and 121%, respectively. In addition, the I_+M treatment significantly increased the P concentration in the root rather than in the shoot of chives and significantly increased the level of P acquisition by chives, increasing the average yield of chives by 229%. Simultaneously, the I_+M treatment significantly increased the level of HM (except Cd) acquisition by sunflower, enhancing the rhizosphere competition by sunflower over chives, and further reducing the transfer of all six HMs from root to shoot in the chives, and inducing significant decreases in chive shoot HM concentrations compared with the monoculture control. Furthermore, the I_+M treatment decreased the average total concentrations and increased the average DTPA-extractable concentrations of soil HMs. The results demonstrate the multifunctional role of AM fungi in the intercropping system for both vegetable production and phytoremediation on HM-contaminated soils.

Comparative assessment of autochthonous bacterial and fungal communities and microbial biomarkers of polluted agricultural soils of the Terra dei Fuochi

Organic and inorganic xenobiotic compounds can affect the potential ecological function of the soil, altering its biodiversity. Therefore, the response of microbial communities to environmental pollution is a critical issue in soil ecology. Here, a high-throughput sequencing approach was used to investigate the indigenous bacterial and fungal community structure as well as the impact of pollutants on their diversity and richness in contaminated and noncontaminated soils of a National Interest Priority Site of Campania Region (Italy) called "Terra dei Fuochi". The microbial populations shifted in the polluted soils via their mechanism of adaptation to contamination, establishing a new balance among prokaryotic and eukaryotic populations. Statistical analyses showed that the indigenous microbial communities were most strongly affected by contamination rather than by site of origin. Overabundant taxa and Actinobacteria were identified as sensitive biomarkers for assessing soil pollution and could provide general information on the health of the environment. This study has important implications for microbial ecology in contaminated environments, increasing our knowledge of the capacity of natural ecosystems to develop microbiota adapted to polluted soil in sites with high agricultural potential and providing a possible approach for modeling pollution indicators for bioremediation purposes.

Metagenomic analysis of rhizosphere microflora of oil-contaminated soil planted with barley and alfalfa

The role of rhizosphere microbial communities in the degradation of hydrocarbons remains poorly understood and is a field of active study. We used high throughput sequencing to explore the rhizosphere microbial diversity in the alfalfa and barley planted oil contaminated soil samples. The analysis of 16s rRNA sequences showed Proteobacteria to be the most enriched (45.9%) followed by Bacteriodetes (21.4%) and Actinobacteria (10.4%) phyla. The results also indicated differences in the microbial diversity among the oil contaminated planted soil samples. The oil contaminated planted soil samples showed a higher richness in the microbial flora when compared to that of untreated samples, as indicated by the Chao1 indices. However, the trend was different for the diversity measure, where oil contaminated barley planted soil samples showed slightly lower diversity indices. While the clustering of soil samples grouped the oil contaminated samples within and across the plant types, the clean sandy soil samples formed a separate group. The oil contaminated rhizosphere soil showed an enrichment of known oil-degrading genera, such as Alcanivorax and Aequorivita, later being specifically enriched in the contaminated soil samples planted with barley. Overall, we found a few well known oil-degrading bacterial groups to be enriched in the oil contaminated planted soil samples compared to the untreated samples. Further, phyla such as Thermi and Gemmatimonadetes showed an enrichment in the oil contaminated soil samples, indicating their potential role in hydrocarbon degradation. The findings of the current study will be useful in understanding the rhizosphere microflora responsible for oil degradation and thus can help in designing appropriate phytoremediation strategies for oil contaminated lands.

Planktonic fungal community structures and their relationship to water quality in the Danjiangkou Reservoir, China

Planktonic fungi are important components of aquatic ecosystems, and analyses of their community composition and function have far-reaching significance for the ecological management and maintenance of reservoir environments. However, few studies have investigated the composition, distribution, and function of planktonic fungi in reservoir ecosystems and their relationship with water quality. Here, the composition of the planktonic fungal community in the surface water layer of the Danjiangkou Reservoir is investigated using Illumina MiSeq sequencing. According to the results, the reservoir community is primarily composed of 7 phyla, including Ascomycota, Rozellomycota, Basidiomycota, Chytridiomycota, and Zygomycota, comprising 294 genera, demonstrating the rich diversity of this community. Redundancy analysis (RDA) of the planktonic fungal community and environmental factors showed dissolved oxygen (DO), chemical oxygen demand (COD), total nitrogen (TN), chlorophyll a (Chl a), and permanganate (CODMn) to be important factors influencing the distribution of planktonic fungi. Spearman correlation analysis of the planktonic fungal community composition and diversity indices with physical and chemical water quality parameters showed that the impacts of TN, COD and DO were the most significant. The results of this study on the planktonic fungal community in the Danjiangkou Reservoir area using high-throughput sequencing revealed that the community is sensitive to water quality parameters. This result provides a reference for studying the composition and distribution of the planktonic fungal community in Danjiangkou Reservoir and its role in the biogeochemical cycle.