Microbial expression profiles in the rhizosphere of willows depend on soil contamination

Rhizospheric Plant-Microbe Interactions: miRNAs as a Key Mediator

The importance of microorganisms in plant development, nutrition, and stress resistance is unquestioned and has led to a more holistic approach of plant-microbe interactions, under the holobiont concept. The structure of the plant microbiota is often described as host driven, especially in the rhizosphere, where microbial communities are shaped by diverse rhizodeposits. Gradually, this anthropogenic vision is fading and being replaced by the idea that plants and microorganisms co-shape the plant microbiota. Through coevolution, plants and microbes have developed cross-kingdom communication channels. Here, we propose that miRNAs are crucial mediators of plant-microbe interactions and microbiota shaping in the rhizosphere. Moreover, we suggest, as an alternative to generally unsuccessful strategies based on microbial inoculants, miRNAs as a promising tool for novel holobiont engineering.

Rhizoremediation as a green technology for the remediation of petroleum hydrocarbon-contaminated soils

Rhizoremediation is increasingly becoming a green and sustainable alternative to physico-chemical methods for remediation of contaminated environments through the utilization of symbiotic relationship between plants and their associated soil microorganisms in the root zone. The overall efficiency can be enhanced by identifying suitable plant-microbe combinations for specific contaminants and supporting the process with the application of appropriate soil amendments. This approach not only involves promoting the existing activity of plants and soil microbes, but also introduces an adequate number of microorganisms with specific catabolic activity. Here, we reviewed recent literature on the main mechanisms and key factors in the rhizoremediation process with a particular focus on soils contaminated with total petroleum hydrocarbon (TPH). We then discuss the potential of different soil amendments to accelerate the remediation efficiency based on biostimulation and bioaugmentation processes. Notwithstanding some successes in well-controlled environments, rhizoremediation of TPH under field conditions is still not widespread and considered less attractive than physico-chemical methods. We catalogued the major pitfalls of this remediation approach at the field scale in TPH-contaminated sites and, provide some applicable situations for the future successful use of in situ rhizoremediation of TPH-contaminated soils.

Soil Characteristics Constrain the Response of Microbial Communities and Associated Hydrocarbon Degradation Genes during Phytoremediation

Rhizodegradation is a promising cleanup technology where microorganisms degrade soil contaminants in the rhizosphere. A symbiotic relationship is expected to occur between plant roots and soil microorganisms in contaminated soils that enhances natural microbial degradation. However, little is known about how different initial microbiotas influence the rhizodegradation outcome. Recent studies have hinted that soil initial diversity has a determining effect on the outcome of contaminant degradation. To test this, we either planted (P) or not (NP) balsam poplars (Populus balsamifera) in two soils of contrasting diversity (agricultural and forest) that were contaminated or not with 50 mg kg^-1 of phenanthrene (PHE). The DNA from the rhizosphere of the P and the bulk soil of the NP pots was extracted and the bacterial genes encoding the 16S rRNA, the PAH ring-hydroxylating dioxygenase alpha subunits (PAH-RHDα) of Gram-positive and Gram-negative bacteria, and the fungal ITS region were sequenced to characterize the microbial communities. The abundances of the PAH-RHDα genes were quantified by real-time quantitative PCR. Plant presence had a significant effect on PHE degradation only in the forest soil, whereas both NP and P agricultural soils degraded the same amount of PHE. Fungal communities were mainly affected by plant presence, whereas bacterial communities were principally affected by the soil type, and upon contamination the dominant PAH-degrading community was similarly constrained by soil type. Our results highlight the crucial importance of soil microbial and physicochemical characteristics in the outcome of rhizoremediation.IMPORTANCE Polycyclic aromatic hydrocarbons (PAH) are a group of organic contaminants that pose a risk to ecosystems' health. Phytoremediation is a promising biotechnology with the potential to restore PAH-contaminated soils. However, some limitations prevent it from becoming the remediation technology of reference, despite being environmentally friendlier than mainstream physicochemical alternatives. Recent reports suggest that the original soil microbial diversity is the key to harnessing the potential of phytoremediation. Therefore, this study focused on determining the effect of two different soil types in the fate of phenanthrene (a polycyclic aromatic hydrocarbon) under balsam poplar remediation. Poplar increased the degradation of phenanthrene in forest, but not in agricultural soil. The fungi were affected by poplars, whereas total bacteria and specific PAH-degrading bacteria were constrained by soil type, leading to different degradation patterns between soils. These results highlight the importance of performing preliminary microbiological studies of contaminated soils to determine whether plant presence could improve remediation rates or not.

Arsenic uptake, speciation and physiological response of tree species (Acer pseudoplatanus, Betula pendula and Quercus robur) treated with dimethylarsinic acid

The aim of the study was to evaluate the effect of dimethylarsinic acid (DMA) on growth parameters and levels of stress-related metabolites in Acer pseudoplatanus, Betula pendula and Quercus robur. The increase of DMA concentration in the solution led to a notable growth retardation of trees. An intense As accumulation (mainly As(III) and As(V)) expressed as BCF and TF > 1 was recorded only for Q. robur. Generally a decrease in contents of cellulose, hemicellulose and holocellulose with a simultaneous increase in lignin content were recorded. Phenolic composition of leaf extracts was modified by DMA, while root and rhizosphere extracts were poor in phenolics. Toxicity of DMA leads to a significant drop in salicylic acid content in leaves observed at lower doses. Higher DMA levels caused a second, probably ROS-derived depletion of the metabolite accompanied with a severe growth retardation, most pronounced in the case of B. pendula. DMA caused the inhibition of LMWOA biosynthesis in roots of A. pseudoplatanus, B. pendula and their exudation into the rhizosphere, while in Q. robur roots and leaves a stimulation of their accumulation was observed. Disturbances in the activity of enzymatic antioxidants were observed for all the species following the increasing level of DMA.

Bioaugmenting the poplar rhizosphere to enhance treatment of 1,4-dioxane

1,4-Dioxane is a highly mobile and persistent groundwater pollutant that often forms large dilute plumes. Because of this, utilizing aggressive pump-and-treat and ex-situ technologies such as advanced oxidation can be prohibitively expensive. In this study, we bioaugmented the poplar rhizosphere with dioxane-degrading bacteria Mycobacterium dioxanotrophicus PH-06 or Pseudonocardia dioxanivorans CB1190 to enhance treatment of 1,4-dioxane in bench-scale experiments. All treatments tested removed 10 mg/L dioxane to near health advisory levels (<4 μg/L). However, PH-06-bioaugmented poplar significantly outperformed all other treatments, reaching <4 μg/L in only 13 days. Growth curve experiments confirmed that PH-06 could not utilize root extract as an auxiliary carbon source for growth. Despite this limitation, our findings suggest that PH-06 is a strong bioaugmentation candidate to enhance the treatment of dioxane by phytoremediation. In addition, we confirmed that CB1190 could utilize both 1,4-dioxane and root extract as substrates. Finally, we demonstrated the large-scale production of these two strains for use in the field. Overall, this study shows that combining phytoremediation and bioaugmentation is an attractive strategy to treat dioxane-contaminated groundwater to low risk-based concentrations (~1 μg/L).

A novel extracellular enzyme stoichiometry method to evaluate soil heavy metal contamination: Evidence derived from microbial metabolic limitation

Heavy metal contaminates have become a significant threat to soil ecosystems due to their chronicity and universality in soil. Soil microbial metabolism plays a vital role in biogeochemical cycles and soil functions. However, the response of microbial metabolism to heavy metal contamination in soil remains elusive despite potentially offering important insight into the health and ecological consequences of soil ecosystems under such contamination. This study used extracellular enzyme stoichiometry models to identify the response of microbial metabolism to various heavy metal contaminants, while also revealing potential implications of heavy metal contaminates in soil ecosystems. Results showed that microbial metabolism was restricted by soil carbon (C) and phosphorus (P) within a heavy metal polluted area in Northwest China. Heavy metal stress significantly increased microbial C limitation while decreasing microbial P limitation. However, microbial C and P limitations both responded consistently to different heavy metals (i.e., Cd, Pb, Zn, and Cu). Heavy metals had the greatest effect on microbial C limitation (i.e., 0.720 of the total effects) compared to other soil properties, and soil with the lowest heavy metal concentration exhibited the lowest microbial C limitation, and vice versa. These results indicated that microbial metabolic limitation can robustly and sensitively reflect the degree of heavy metals pollution in soil. Additionally, increased microbial C limitation caused by heavy metal contaminants could potentially escalate C release by promoting soil C decomposition as well as increasing investments in enzyme production and the maintenance of metabolic processes. Consequently, potential C loss induced by heavy metal pollution on soil ecosystems may be extensive and significant. Generally, our results suggest the usefulness of extracellular enzyme stoichiometry as a new method from which to evaluate heavy metal soil pollution, while microbial metabolic limitation could potentially be a promising indicator.

Distinct rhizobacterial functional assemblies assist two Sedum alfredii ecotypes to adopt different survival strategies under lead stress

Lead (Pb) contamination presents a widespread environmental plague. Sedum alfredii is widely used for soil phytoremediation owing to its capacity to extract heavy metals, such as Pb. Although efficient Pb extraction is mediated by complex interactions between the roots and rhizospheric bacteria, the mechanism by which S. alfredii recruits microorganisms under Pb stress remains unclear. The Pb-accumulating ecotype (AE) and non-accumulating ecotype (NAE) of S. alfredii recruited different rhizobacterial communities. Under Pb stress, AE rhizosphere-enriched bacteria assembled into stable-connected clusters with higher phylogenetic and functional diversity. These microbes, e.g., Flavobacterium, could release indoleacetic acid to promote plant growth and siderophores, thereby increasing Pb availability. The NAE rhizosphere-enriched functional bacteria "desperately" assembled into highly specialized functional clusters with extremely low phylogenetic diversity. These bacteria, e.g., Pseudomonas, could enhance phosphorus solubilization and Pb precipitation, thereby reducing Pb stress and plant Pb accumulation. High niche overlap level of the rhizo-enriched species raised challenges in soil resource utilization, whereas the NAE community assembly was markedly constrained by environmental "selection effect" than that of AE rhizobacterial community. These results indicate that different ecotypes of S. alfredii recruit distinct bacterial functional assemblies to drive specific plant-soil feedbacks for different survival in Pb-contaminated soils. To cope with heavy metal stress, NAE formed a highly functional and specialized but vulnerable community and efficiently blocked heavy metal absorption by plants. However, the AE community adopted a more stable and elegant strategy to promote plant growth and the accumulation of dry matter via multiple evolutionary strategies that ensured a high yield of heavy metal phytoextraction. This for the first time provides new insights into the roles of rhizosphere microbes in plant adaptations to abiotic stresses.

Deciphering the Omics of Plant-Microbe Interaction: Perspectives and New Insights

Introduction

Plants do not grow in isolation, rather they are hosts to a variety of microbes in their natural environments. While, few thrive in the plants for their own benefit, others may have a direct impact on plants in a symbiotic manner. Unraveling plant-microbe interactions is a critical component in recognizing the positive and negative impacts of microbes on plants. Also, by affecting the environment around plants, microbes may indirectly influence plants. The progress in sequencing technologies in the genomics era and several omics tools has accelerated in biological science. Studying the complex nature of plant-microbe interactions can offer several strategies to increase the productivity of plants in an environmentally friendly manner by providing better insights. This review brings forward the recent works performed in building omics strategies that decipher the interactions between plant-microbiome. At the same time, it further explores other associated mutually beneficial aspects of plant-microbe interactions such as plant growth promotion, nitrogen fixation, stress suppressions in crops and bioremediation; as well as provides better insights on metabolic interactions between microbes and plants through omics approaches. It also aims to explore advances in the study of Arabidopsis as an important avenue to serve as a baseline tool to create models that help in scrutinizing various factors that contribute to the elaborate relationship between plants and microbes. Causal relationships between plants and microbes can be established through systematic gnotobiotic experimental studies to test hypotheses on biologically derived interactions.

Conclusion

This review will cover recent advances in the study of plant-microbe interactions keeping in view the advantages of these interactions in improving nutrient uptake and plant health.

Co-inoculation effect of plant-growth-promoting rhizobacteria and rhizobium on EDDS assisted phytoremediation of Cu contaminated soils

Chelants application can increase the bioavailability of metals, subsequently limiting plant growth and reducing the efficiency of phytoremediation. Plant growth-promoting rhizobacteria (PGPRs) and rhizobium have substantial potential to improve plant growth and plant tolerance to metal stress. We evaluated the effects of co-inoculation with a PGPR strain (Paenibacillus mucilaginosus) and a Cu-resistant rhizobium strain (Sinorhizobium meliloti) on the efficiency of biodegradable chelant (S,S-ethylenediaminedisuccinic acid; EDDS) assisted phytoremediation of a Cu contaminated soil using alfalfa. The highest total Cu extraction by alfalfa was observed in the EDDS-treated soil upon co-inoculation with the PGPR and rhizobium strains, which was 1.2 times higher than that without co-inoculation. Partial least squares path modeling identified plant oxidative damage and soil microbial biomass as the key variables influencing Cu uptake by alfalfa roots. Co-inoculation significantly reduced the oxidative damage to alfalfa by mitigating the accumulation of malondialdehyde and reactive oxygen species, and improving the antioxidation capacity of the plant in the presence of EDDS. EDDS application decreased microbial diversity in the rhizosphere, whereas co-inoculation increased microbial biomass carbon and nitrogen, and microbial community diversity. Increased relative abundances of Actinobacteria and Bacillus and the presence of Firmicutes taxa as potential biomarkers demonstrated that co-inoculation increased soil nutrient content, and improved plant growth. Co-inoculation with PGPR and rhizobium can be useful for altering plant-soil biochemical responses during EDDS-enhanced phytoremediation to alleviate phytotoxicity of heavy metals and improve soil biochemical activities. This study provides an effective strategy for improving phytoremediation efficiency and soil quality during chelant assisted phytoremediation of metal-contaminated soils.

The invisible life inside plants: Deciphering the riddles of endophytic bacterial diversity

Endophytic bacteria often promote plant growth and protect their host plant against pathogens, herbivores, and abiotic stresses including drought, increased salinity or pollution. Current agricultural practices are being challenged in terms of climate change and the ever-increasing demand for food. Therefore, the rational exploitation of bacterial endophytes to increase the productivity and resistance of crops appears to be very promising. However, the efficient and larger-scale use of bacterial endophytes for more effective and sustainable agriculture is hindered by very little knowledge on molecular aspects of plant-endophyte interactions and mechanisms driving bacterial communities in planta. In addition, since most of the information on bacterial endophytes has been obtained through culture-dependent techniques, endophytic bacterial diversity and its full biotechnological potential still remain highly unexplored. In this study, we discuss the diversity and role of endophytic populations as well as complex interactions that the endophytes have with the plant and vice versa, including the interactions leading to plant colonization. A description of biotic and abiotic factors influencing endophytic bacterial communities is provided, along with a summary of different methodologies suitable for determining the diversity of bacterial endophytes, mechanisms governing the assembly and structure of bacterial communities in the endosphere, and potential biotechnological applications of endophytes in the future.

Rhizosphere microbiome: Engineering bacterial competitiveness for enhancing crop production

Plants in nature are constantly exposed to a variety of abiotic and biotic stresses which limits their growth and production. Enhancing crop yield and production to feed exponentially growing global population in a sustainable manner by reduced chemical fertilization and agrochemicals will be a big challenge. Recently, the targeted application of beneficial plant microbiome and their cocktails to counteract abiotic and biotic stress is gaining momentum and becomes an exciting frontier of research. Advances in next generation sequencing (NGS) platform, gene editing technologies, metagenomics and bioinformatics approaches allows us to unravel the entangled webs of interactions of holobionts and core microbiomes for efficiently deploying the microbiome to increase crops nutrient acquisition and resistance to abiotic and biotic stress. In this review, we focused on shaping rhizosphere microbiome of susceptible host plant from resistant plant which comprises of specific type of microbial community with multiple potential benefits and targeted CRISPR/Cas9 based strategies for the manipulation of susceptibility genes in crop plants for improving plant health. This review is significant in providing first-hand information to improve fundamental understanding of the process which helps in shaping rhizosphere microbiome.

Potential risks of antibiotic resistant bacteria and genes in bioremediation of petroleum hydrocarbon contaminated soils

Bioremediation represents a sustainable approach to remediating petroleum hydrocarbon contaminated soils. One aspect of sustainability includes the sourcing of nutrients used to stimulate hydrocarbon-degrading microbial populations. Organic nutrients such as animal manure and sewage sludge may be perceived as more sustainable than conventional inorganic fertilizers. However, organic nutrients often contain antibiotic residues and resistant bacteria (along with resistance genes and mobile genetic elements). This is further exacerbated since antibiotic resistant bacteria may become more abundant in contaminated soils due to co-selection pressures from pollutants such as metals and hydrocarbons. We review the issues surrounding bioremediation of petroleum-hydrocarbon contaminated soils, as an example, and consider the potential human-health risks from antibiotic resistant bacteria. While awareness is coming to light, the relationship between contaminated land and antibiotic resistance remains largely under-explored. The risk of horizontal gene transfer between soil microorganisms, commensal bacteria and/or human pathogens needs to be further elucidated, and the environmental triggers for gene transfer need to be better understood. Findings of antibiotic resistance from animal manures are emerging, but even fewer bioremediation studies using sewage sludge have made any reference to antibiotic resistance. Resistance mechanisms, including those to antibiotics, have been considered by some authors to be a positive trait associated with resilience in strains intended for bioremediation. Nevertheless, recognition of the potential risks associated with antibiotic resistant bacteria and genes in contaminated soils appears to be increasing and requires further investigation. Careful selection of bacterial candidates for bioremediation possessing minimal antibiotic resistance as well as pre-treatment of organic wastes to reduce selective pressures (e.g., antibiotic residues) are suggested to prevent environmental contamination with antibiotic-resistant bacteria and genes.

Mechanisms of water regime effects on uptake of cadmium and nitrate by two ecotypes of water spinach (Ipomoea aquatica Forsk.) in contaminated soil

Availability of cadmium (Cd) and nitrate and their transfer to green leafy vegetables is highly dependent on physical, chemical and biochemical conditions of the soil. The phenotypic characteristics, accumulation of hazardous materials and rhizosphere properties of two ecotypes of water spinach in response to water stress were investigated. Flooding significantly enhanced plant growth and decreased Cd and nitrate concentrations in the shoot and root of both ecotypes of water spinach. Flooding extensively changed the physicochemical properties and biological processes in the rhizosphere, including increased pH and activities of urease and acid phosphatase, and decreased availability of Cd and nitrate and activity of nitrate reductase. Furthermore, flooding increased rhizosphere bacteria community diversity (including richness and evenness) and changed their community structure. Denitrifying bacteria (Clostridiales, Azoarcus and Pseudomonas), toxic metal resistant microorganisms (Rhodosporillaceae, Rhizobiales and Geobacter) were enriched in the rhizosphere under flooding conditions, and the plant growth-promoting taxa (Sphingomonadaceae) were preferentially colonized in the high accumulator (HA) rhizosphere region. These results indicated that flooding treatments result in biochemical and microbiological changes in soil, especially in the rhizosphere and reduced the availability of Cd and nitrate to plants, thus decreasing their uptake by water spinach. It is, therefore, possible to promote crop growth and reduce the accumulation of hazardous materials in vegetable crops like water spinach by controlling soil moisture conditions.

Removal Efficiencies of Constructed Wetland Planted with Phragmites and Vetiver in Treating Synthetic Wastewater Contaminated with High Concentration of PAHs

This study aimed to evaluate the capability of horizontal subsurface flow constructed wetlands (HSFCWs) in treating contaminated wastewater with a high concentration of polycyclic aromatic hydrocarbons (PAHs) (Phenanthrene, Pyrene, and Benzo[a]Pyrene), using two plants, namely Phragmites and Vetiver. The investigated parameters were (1) PAHs uptake by the plants, (2) PAHs removal efficiencies, (3) accumulated PAHs in the soil of CWs, (4) shoot/root concentration factor, (5) translocation factor, and (6) PAHs correlation to lipid contains in the plants. During the treatment period, the results showed that the highest concentration of Phenanthrene in the shoot and the root systems of Phragmites, was 229.3 and 192 μg/g; Pyrene was 69.1 and 59.2 µg/g; and Benzo[a]Pyrene 25.1 and 20.2 µg/g, respectively. Meanwhile, in the Vetiver shoot and root systems were Phenanthrene 87.5 and 64.1 µg/g; Pyrene 63.2 and 42.1 µg/g; and Benzo[a]Pyrene 21.3 and 27.3 µg/g, respectively. The removal rates of Phenanthrene, Pyrene, and Benzo[a]Pyrene (PAHs compounds) by the CW planted with Phragmites were found to be 83%, 71%, and 81%, respectively, while the removal rates by CW planted with Vetiver were found to be 67%, 66%, and 73%, respectively. Moreover, the removal rates by unplanted CW were found to be 62%, 58%, and 55%, respectively. The results indicated that the HSFCW planted with Phragmites has an effective pathway to remove high concentrations of PAHs.

Niche differentiation is spatially and temporally regulated in the rhizosphere

The rhizosphere is a hotspot for microbial carbon transformations, and is the entry point for root polysaccharides and polymeric carbohydrates that are important precursors to soil organic matter (SOM). However, the ecological mechanisms that underpin rhizosphere carbohydrate depolymerization are poorly understood. Using Avena fatua, a common annual grass, we analyzed time-resolved metatranscriptomes to compare microbial functions in rhizosphere, detritusphere, and combined rhizosphere-detritusphere habitats. Transcripts were binned using a unique reference database generated from soil isolate genomes, single-cell amplified genomes, metagenomes, and stable isotope probing metagenomes. While soil habitat significantly affected both community composition and overall gene expression, the succession of microbial functions occurred at a faster time scale than compositional changes. Using hierarchical clustering of upregulated decomposition genes, we identified four distinct microbial guilds populated by taxa whose functional succession patterns suggest specialization for substrates provided by fresh growing roots, decaying root detritus, the combination of live and decaying root biomass, or aging root material. Carbohydrate depolymerization genes were consistently upregulated in the rhizosphere, and both taxonomic and functional diversity were highest in the combined rhizosphere-detritusphere, suggesting coexistence of rhizosphere guilds is facilitated by niche differentiation. Metatranscriptome-defined guilds provide a framework to model rhizosphere succession and its consequences for soil carbon cycling.

Soil exposed to silver nanoparticles reveals significant changes in community structure and altered microbial transcriptional profiles

Anthropogenic activities can disrupt soil ecosystems, normally resulting in reduced soil microbial health. Regulatory agencies need to determine the effects of uncharacterized substances on soil microbial health to establish the safety of these chemicals if they end up in the environment. Previous work has focused on measuring traditional ecotoxicologial endpoints within the categories of microbial biomass, activity, and community structure/diversity. Because these tests can be labor intensive, lengthy to conduct, and cannot measure changes in individual gene functions, we wanted to establish whether metatranscriptomics could be used as a more sensitive endpoint and provide a perspective on community function that is more informative than taxonomic identification of microbes alone. We spiked a freshly collected sandy loam soil (Vulcan, Alberta, Canada) with 0, 60, 145, 347, 833, and 2000 mg kg^-1 of silver nanoparticles (AgNPs), a known antagonist of microorganisms due to its propensity for dissolution of toxic silver ions. Assessments performed in our previous work using traditional tests demonstrated the toxicity of AgNPs on soil microbial processes. We expanded this analysis with genomics-based tests by measuring changes in community taxonomic structure and function using 16S rDNA profiling and metatranscriptomics. In addition to identifying bacterial taxa affected by AgNPs, we found that genes involved in heavy metal resistance (e.g., the CzcA efflux pump) and other toxicity response pathways were highly upregulated in the presence of silver. Dose-response analysis using BMDExpress2 software successfully modeled many physiologically relevant genes responding to low concentrations of AgNPs. We found that the transcriptomic point of departure (BMD₅₀) was lower than the IC50s calculated using the traditional tests in our previous work. These results suggest that dose-response modeling of metatranscriptomic gene expression is a useful tool in soil microbial health assessment. SUMMARY: Genomics-based endpoints for the assessment of soil microbial health can be used to perform quantitative dose-response modeling, and soil-based RNAseq adds functional insights.

Distribution of Medically Relevant Antibiotic Resistance Genes and Mobile Genetic Elements in Soils of Temperate Forests and Grasslands Varying in Land Use

Antibiotic-resistant pathogens claim the lives of thousands of people each year and are currently considered as one of the most serious threats to public health. Apart from clinical environments, soil ecosystems also represent a major source of antibiotic resistance determinants, which can potentially disseminate across distinct microbial habitats and be acquired by human pathogens via horizontal gene transfer. Therefore, it is of global importance to retrieve comprehensive information on environmental factors, contributing to an accumulation of antibiotic resistance genes and mobile genetic elements in these ecosystems. Here, medically relevant antibiotic resistance genes, class 1 integrons and IncP-1 plasmids were quantified via real time quantitative PCR in soils derived from temperate grasslands and forests, varying in land use over a large spatial scale. The generated dataset allowed an analysis, decoupled from regional influences, and enabled the identification of land use practices and soil characteristics elevating the abundance of antibiotic resistance genes and mobile genetic elements. In grassland soils, the abundance of the macrolide resistance gene mefA as well as the sulfonamide resistance gene sul2 was positively correlated with organic fertilization and the abundance of aac(6')-lb, conferring resistance to different aminoglycosides, increased with mowing frequency. With respect to forest soils, the beta-lactam resistance gene blaIMP-12 was significantly correlated with fungal diversity which might be due to the fact that different fungal species can produce beta-lactams. Furthermore, except blaIMP-5 and blaIMP-12, the analyzed antibiotic resistance genes as well as IncP-1 plasmids and class-1 integrons were detected less frequently in forest soils than in soils derived from grassland that are commonly in closer proximity to human activities.

Ethanol-blended petroleum fuels: implications of co-solvency for phytotechnologies

In recent decades, there has been increasing interest in the use of ethanol-blended fuels as alternatives to unblended fossil fuels. These initiatives are targeted at combating CO₂ and particulate matter emissions, as these oxygenates leave behind a lesser carbon footprint. Noble as it may appear, this innovation is not without attendant ugly consequences. One major implication is the effect of co-solvency on the applicability of various forms of phytotechnologies for contaminant removal. By means of gas chromatography-mass spectrometry, this research investigated the effect of diesel fuel ethanol addition on the leaching potentials of petroleum hydrocarbons. Since phytoremediation of hydrocarbons depends largely on rhizodegradation of contaminants by the root-associated microbiome, the leaching of petroleum hydrocarbons beyond the rooting zones of plants may limit the effectiveness of this process as a reclamation strategy for ethanol-blended fuel spills. The analyses presented in this paper highlight the need for energy scientists to carefully consider the environmental impacts of ethanol-blended innovations holistically.

Ethanol addition to diesel fuels significantly affects the leaching potentials of petroleum hydrocarbons, thereby making them inaccessible to rhizoremediation.

Silicate Fertilizer Amendment Alters Fungal Communities and Accelerates Soil Organic Matter Decomposition

Soil microorganisms play a crucial role in organic matter decomposition and nutrient cycling in cropping systems. Compared to bacteria, fungal community composition and the role of fungi in organic matter decomposition and nutrient cycling in agro-systems are, however, elusive. Silicon (Si) fertilization is essential to improve agronomic performance of rice. The effects of the Si fertilizer application on the soil fungal community composition and their contribution in soil organic matter (SOM) decomposition are not yet studied. We investigated the short-term (120 days) slag silicate fertilizer (SSF) amendment impacts on plant photosynthesis and soil biochemical changes, soil fungal communities (assessed by ITS amplicon illumina sequencing), hydrolytic and oxidase enzyme activities, CO₂ emissions, and bacterial and fungal respiration in diverse eco-geographic races of rice (Oryza sativa L.), i.e., Japonica rice (O. sativa japonica) and Indica rice (O. sativa indica). The short-term SSF amendment significantly increased the relative abundance of saprotrophic fungi and accelerated organic matter decomposition. The increase in saprotrophic fungi was mostly attributed to greater labile C availability and Si availability. Higher organic matter decomposition was accompanied by an increase in both hydrolytic and oxidative enzyme activities in response to the SSF amendment. The stimulation of oxidative enzyme activities was explained by an increase in root oxidase activities and iron redox cycling, whereas stimulation of hydrolytic enzyme activities was explained by the greater labile C availability under SSF fertilization. We conclude that the short-term SSF amendment increases saprotrophic fungal communities and soil hydrolytic and oxidative enzyme activities, which in turn stimulates SOM mineralization and thus could have negative feedback impacts on soil C storage in submerged rice paddies.

Variation in pickleweed root-associated microbial communities at different locations of a saline solid waste management unit contaminated with petroleum hydrocarbons

The main purpose of this study was to explore the potential influences of pickleweed vegetation on the abundance, diversity and metabolic activities of microbial communities in four distinct areas of a petroleum-contaminated solid waste management unit (SWMU) located in Contra Costa County, northern California. The four areas sampled include two central areas, one of which is central vegetated (CV) and one unvegetated (UV), and two peripheral vegetated areas, one of which is located to the west side of the SWMU (V-West) and one located to the east side (V-East). Measurements were made of total petroleum hydrocarbons (TPH), polyaromatic hydrocarbons (PAH), soil physicochemical properties, and various aspects of microbial communities including metabolic activities, microbial abundances (PLFAs), diversity and composition based on amplicon sequencing. The peripheral V-East and V-West sites had 10-times lower electrical conductivity (EC) than that of the CV and UV sites. The high salinity levels of the CV and UV sites were associated with significant reductions in bacterial and fungal abundances (PLFA) when compared to V-East but not when compared to V-West. TPH levels of CV and UV were not significantly different from those of V-West but were substantially lower than V-East TPH (19,311 mg/kg of dry soil), the high value of which may have been associated with a pipeline that ran through the area. Microbial activities (in terms of soil respiration and the activities of three soil enzymes, i.e., urease, lipase, and phosphatase) were greatest in the vegetated sites compared to the UV site. The prokaryotic community was not diverse as revealed by the Shannon index with no significant variation among the four groups of samples. However, the fungal community of the peripheral sites, V-East and V-West had significantly higher OTU richness and Shannon index. Structure of prokaryotic communities inhabiting the rhizosphere of pickleweed plants at the three sites differed significantly and were also different from those found in the UV region of the central site according to pairwise, global PERMANOVA and ANOSIM analyses. The differences in OTU-based rhizosphere-associated bacterial and fungal communities’ composition were explained mainly by the changes in soil EC and pH. The results suggest that saline TPH-contaminated areas that are vegetated with pickleweed are likely to have increased abundances, diversity and metabolic activities in the rhizosphere compared to unvegetated areas, even in the presence of high salinity.

Insights into Biodegradation Related Metabolism in an Abnormally Low Dissolved Inorganic Carbon (DIC) Petroleum-Contaminated Aquifer by Metagenomics Analysis

In petroleum-contaminated aquifers, biodegradation is always associated with various types of microbial metabolism. It can be classified as autotrophic (such as methanogenic and other carbon fixation) and heterotrophic (such as nitrate/sulfate reduction and hydrocarbon consumption) metabolism. For each metabolic type, there are several key genes encoding the reaction enzymes, which can be identified by metagenomics analysis. Based on this principle, in an abnormally low dissolved inorganic carbon (DIC) petroleum-contaminated aquifer in North China, nine groundwater samples were collected along the groundwater flow, and metagenomics analysis was used to discover biodegradation related metabolism by key genes. The major new finding is that autotrophic metabolism was revealed, and, more usefully, we attempt to explain the reasons for abnormally low DIC. The results show that the methanogenesis gene, Mcr, was undetected but more carbon fixation genes than nitrate reduction and sulfate genes were found. This suggests that there may be a considerable number of autotrophic microorganisms that cause the phenomenon of low concentration of dissolved inorganic carbon in contaminated areas. The metagenomics data also revealed that most heterotrophic, sulfate, and nitrate reduction genes in the aquifer were assimilatory sulfate and dissimilatory nitrate reduction genes. Although there was limited dissolved oxygen, aerobic degrading genes AlkB and Cdo were more abundant than anaerobic degrading genes AssA and BssA. The metagenomics information can enrich our microorganic knowledge about petroleum-contaminated aquifers and provide basic data for further bioremediation.

Plant Identity Shaped Rhizospheric Microbial Communities More Strongly Than Bacterial Bioaugmentation in Petroleum Hydrocarbon-Polluted Sediments

Manipulating the plant-root microbiota has the potential to reduce plant stress and promote their growth and production in harsh conditions. Community composition and activity of plant-roots microbiota can be either beneficial or deleterious to plant health. Shifting this equilibrium could then strongly affect plant productivity in anthropized areas. In this study, we tested whether repeated bioaugmentation with Proteobacteria influenced plant productivity and the microbial communities associated with the rhizosphere of four plant species growing in sediments contaminated with petroleum hydrocarbons (PHCs). A mesocosm experiment was performed in randomized block design with two factors: (1) presence or absence of four plants species collected from a sedimentation basin of a former petrochemical plant, and (2) bioaugmentation or not with a bacterial consortium composed of ten isolates of Proteobacteria. Plants were grown in a greenhouse over 4 months. MiSeq amplicon sequencing, targeting the bacterial 16S rRNA gene and the fungal ITS, was used to assess microbial community structures of sediments from planted or unplanted microcosms. Our results showed that while bioaugmentation caused a significant shift in microbial communities, presence of plant and their species identity had a stronger influence on the structure of the microbiome in PHCs contaminated sediments. The outcome of this study provides knowledge on the diversity and behavior of rhizosphere microbes associated with indigenous plants following repeated bioaugmentation, underlining the importance of plant selection in order to facilitate their efficient management, in order to accelerate processes of land reclamation.

Heavy Metal Pollutions: State of the Art and Innovation in Phytoremediation

Mineral nutrition of plants greatly depends on both environmental conditions, particularly of soils, and the genetic background of the plant itself. Being sessile, plants adopted a range of strategies for sensing and responding to nutrient availability to optimize development and growth, as well as to protect their metabolisms from heavy metal toxicity. Such mechanisms, together with the soil environment, meaning the soil microorganisms and their interaction with plant roots, have been extensively studied with the goal of exploiting them to reclaim polluted lands; this approach, defined phytoremediation, will be the subject of this review. The main aspects and innovations in this field are considered, in particular with respect to the selection of efficient plant genotypes, the application of improved cultural strategies, and the symbiotic interaction with soil microorganisms, to manage heavy metal polluted soils.

Stable isotope probing and metagenomics highlight the effect of plants on uncultured phenanthrene-degrading bacterial consortium in polluted soil

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous soil pollutants. The discovery that plants can stimulate microbial degradation of PAHs has promoted research on rhizoremediation strategies. We combined DNA-SIP with metagenomics to assess the influence of plants on the identity and metabolic functions of active PAH-degrading bacteria in contaminated soil, using phenanthrene (PHE) as a model hydrocarbon. 13C-PHE dissipation was 2.5-fold lower in ryegrass-planted conditions than in bare soil. Metabarcoding of 16S rDNA revealed significantly enriched OTUs in 13C-SIP incubations compared to 12C-controls, namely 130 OTUs from bare soil and 73 OTUs from planted soil. Active PHE-degraders were taxonomically diverse (Proteobacteria, Actinobacteria and Firmicutes), with Sphingomonas and Sphingobium dominating in bare and planted soil, respectively. Plant root exudates favored the development of PHE-degraders having specific functional traits at the genome level. Indeed, metagenomes of 13C-enriched DNA fractions contained more genes involved in aromatic compound metabolism in bare soil, whereas carbohydrate catabolism genes were more abundant in planted soil. Functional gene annotation allowed reconstruction of complete pathways with several routes for PHE catabolism. Sphingomonadales were the major taxa performing the first steps of PHE degradation in both conditions, suggesting their critical role to initiate in situ PAH remediation. Active PHE-degraders act in a consortium, whereby complete PHE mineralization is achieved through the combined activity of taxonomically diverse co-occurring bacteria performing successive metabolic steps. Our study reveals hitherto underestimated functional interactions for full microbial detoxification in contaminated soils.

Fate of antibiotics and the related antibiotic resistance genes during sludge stabilization in sludge treatment wetlands

Antibiotics contamination and related antibiotics resistance genes (ARGs) in wastewater sludge have been a concern for environmental pollution and human health risk for years. This study investigated the fate of antibiotics and related ARGs in sludge from sludge treatment wetlands (STWs). We examined three sludge treatment beds i.e. unit No.1 was sludge drying bed with aeration tubes; unit No.2 was a ventilated sludge drying reed bed; and the unit No.3 was a sludge drying reed bed without aeration tubes. The targeted antibiotics included oxytetracycline, roxithromycin and azithromycin. The targeted ARGs included tetA, tetC, msrSA and ermB. The results indicated that in all three units antibiotics were removed significantly and related ARGs declined over one year period. The antibiotics concentrations in the surface layer were lower than those in the bottom layer. The highest removal efficiency of the targeted antibiotics was observed in the unit No.2. The removal efficiency of the targeted ARGs influenced by different parameters, especially reeds, aeration tubes and temperature. Correlation analysis between the concentrations of antibiotics and corresponding ARGs showed that in both the bottom and surface layer of all three units, a significant correlation (p < 0.05) was found between the concentrations of roxithromycin and azithromycin and the absolute abundances of msrSA. A significant correlation (p < 0.05) was also observed between the concentrations of oxytetracycline and the absolute abundances of tetA and tetC. The results demonstrated that STWs can effectively reduce the target antibiotics contents and related ARGs; and the STW with reed and aeration tubes performed better.

Taxonomic and functional responses of soil microbial communities to slag-based fertilizer amendment in rice cropping systems

The effective utilization of slag-based Silicon fertilizer (silicate fertilizer) in agriculture to improve crop productivity and to mitigate environmental consequences turns it into a high value added product in sustainable agriculture. Despite the integral role of soil microbiome in agricultural production and virtually all ecosystem processes, our understanding of the microbial role in ecosystem functions and agricultural productivity in response to the silicate fertilizer amendment is, however, elusive. In this study, using 16S rRNA gene and ITS amplicon illumina sequencing and a functional gene microarray, i.e., GeoChip 5, we report for the first time the responses of soil microbes and their functions to the silicate fertilizer amendment in two different geographic races of Oryza sativa var. Japonica (Japonica rice) and var. Indica (Indica rice). The silicate fertilizer significantly increased soil pH, photosynthesis rate, nutrient (i.e., C, Si, Fe, P) availability and crop productivity, but decreased N availability and CH₄ and N₂O emissions. Moreover, the silicate fertilizer application significantly altered soil bacterial and fungal community composition and increased abundance of functional genes involved in labile C degradation, C and N fixation, phosphorus utilization, CH₄ oxidation, and metal detoxification, whereas those involve in CH₄ production and denitrification were decreased. The changes in the taxonomic and functional structure of microbial communities by the silicate fertilizer were mostly regulated by soil pH, plant photosynthesis, and nutrient availability. This study provides novel insights into our understanding of microbial functional processes in response to the silicate fertilizer amendment in rice cropping systems and has important implications for sustainable rice production.

Resilience and Assemblage of Soil Microbiome in Response to Chemical Contamination Combined with Plant Growth

A lack of knowledge of the microbial responses to environmental change at the species and functional levels hinders our ability to understand the intrinsic mechanisms underlying the maintenance of microbial ecosystems. Here, we present results from temporal microcosms that introduced inorganic and organic contaminants into agro-soils for 90 days, with three common legume plants. Temporal dynamics and assemblage of soil microbial communities and functions in response to contamination under the influence of growth of different plants were explored via sequencing of the 16S rRNA amplicon and by shotgun metagenomics. Soil microbial alpha diversity and structure at the taxonomic and functional levels exhibited resilience patterns. Functional profiles showed greater resilience than did taxonomic ones. Different legume plants imposed stronger selection on taxonomic profiles than on functional ones. Network and random forest analyses revealed that the functional potential of soil microbial communities was fostered by various taxonomic groups. Betaproteobacteria were important predictors of key functional traits such as amino acid metabolism, nucleic acid metabolism, and hydrocarbon degradation. Our study reveals the strong resilience of the soil microbiome to chemical contamination and sensitive responses of taxonomic rather than functional profiles to selection processes induced by different legume plants. This is pivotal to develop approaches and policies for the protection of soil microbial diversity and functions in agro-ecosystems with different response strategies from global environmental drivers, such as soil contamination and plant invasion.IMPORTANCE Exploring the microbial responses to environmental disturbances is a central issue in microbial ecology. Understanding the dynamic responses of soil microbial communities to chemical contamination and the microbe-soil-plant interactions is essential for forecasting the long-term changes in soil ecosystems. Nevertheless, few studies have applied multi-omics approaches to assess the microbial responses to soil contamination and the microbe-soil-plant interactions at the taxonomic and functional levels simultaneously. Our study reveals clear succession and resilience patterns of soil microbial diversity and structure in response to chemical contamination. Different legume plants exerted stronger selection processes on taxonomic than on functional profiles in contaminated soils, which could benefit plant growth and fitness as well as foster the potential abilities of hydrocarbon degradation and metal tolerance. These results provide new insight into the resilience and assemblage of soil microbiome in response to environmental disturbances in agro-ecosystems at the species and functional levels.

Effects of Phytoremediation Treatment on Bacterial Community Structure and Diversity in Different Petroleum-Contaminated Soils

Increased exploitation and use of petroleum resources is leading to increased risk of petroleum contamination of soil and groundwater. Although phytoremediation is a widely-used and cost-effective method for rehabilitating soils polluted by petroleum, bacterial community structure and diversity in soils undergoing phytoremediation is poorly understood. We investigate bacterial community response to phytoremediation in two distinct petroleum-contaminated soils (add prepared petroleum-contaminated soils) from northwest China, Weihe Terrace soil and silty loam from loess tableland. High-throughput sequencing technology was used to compare the bacterial communities in 24 different samples, yielding 18,670 operational taxonomic units (OTUs). The dominant bacterial groups, Proteobacteria (31.92%), Actinobacteria (16.67%), Acidobacteria (13.29%) and Bacteroidetes (6.58%), increased with increasing petroleum concentration from 3000 mg/kg–10,000 mg/kg, while Crenarchaeota (13.58%) and Chloroflexi (4.7%) decreased. At the order level, RB41, Actinomycetales, Cytophagales, envOPS12, Rhodospirillales, MND1 and Xanthomonadales, except Nitrososphaerales, were dominant in Weihe Terrace soil. Bacterial community structure and diversity in the two soils were significantly different at similar petroleum concentrations. In addition, the dominant genera were affected by available nitrogen, which is strongly associated with the plants used for remediation. Overall, the bacterial community structure and diversity were markedly different in the two soils, depending on the species of plants used and the petroleum concentration.

Cultivar-specific response of bacterial community to cadmium contamination in the rhizosphere of rice (Oryza sativa L.)

Cadmium accumulation in rice grains is highly dependent on its bioavailability that affected by various physicochemical properties and microbiological processes of soil. The rhizospheric bacterial communities of rice grown in contaminated soils by means of rice cultivars highly or weakly accumulating Cd in grains (HA and LA, respectively) were investigated. HA roots absorbed 7.26- and 2.25-fold more Cd than did LA roots at low (0.44 mg kg^-1) and high (6.66 mg kg^-1) soil Cd levels, respectively. Regardless of Cd levels, Cd bioavailability in the rhizosphere of HA was significantly higher than that of LA. Planting of rice and elevated Cd levels both significantly decreased bacterial α-diversity and altered bacterial community structure, with noticeable differences between the rice cultivars. Taxa specifically enriched in the HA rhizosphere (phyla Bacteroidetes, Firmicutes, and Deltaproteobacteria) can directly or indirectly participate in metal activation, whereas the LA rhizosphere was highly colonized by plant growth-promoting taxa (phyla Alphaproteobacteria and Gammaproteobacteria). The results indicate a potential association of Cd uptake and accumulation with rhizosphere bacteria in rice grown on a contaminated soil, thus providing baseline data and a new perspective on the maintenance of rice security.

High PAH degradation and activity of degrading bacteria during alfalfa growth where a contrasted active community developed in comparison to unplanted soil

PAH biodegradation in plant rhizosphere has been investigated in many studies, but the timescale of degradation and degrading bacteria activity was rarely considered. We explored the impact of plants on the temporal variability of PAH degradation, microbial abundance, activity, and bacterial community structure in a rhizotron experiment. A historically contaminated soil was spiked with PAHs, planted or not with alfalfa, over 22 days with sampling once a week. In both conditions, most of the spiked PAHs were dissipated during the first week, conducting to polar polycyclic aromatic compound production and to decreased richness and diversity of bacterial communities. We showed a rapid impact of the rhizosphere on PAH degradation via the increased activity of PAH-degrading bacteria. After 12 days, PAH degradation was significantly higher in the planted (100% degradation) than in unplanted (70%) soil. Gram-negative (Proteobacteria) PAH-dioxygenase genes and transcripts were higher in planted than unplanted soil and were correlated to the spiked PAH degradation. Conversely, Gram-positive (Actinobacteria) PAH-dioxygenase gene transcription was constant over time in both conditions. At 12 days, plant growth favored the activity of many Gammaproteobacteria (Pseudomonadaceae, Stenotrophomonas, and Acinetobacter) while in unplanted soil Alphaproteobacteria (Sphingomonadaceae, Sphingobium, and Magnetospirillum) and Actinobacteria (Iamia, Geodermatophilaceae, and Solirubrobacterales) were more active.

Rhizoremediation of petroleum hydrocarbons: a model system for plant microbiome manipulation

Phytoremediation is a green and sustainable alternative to physico-chemical methods for contaminated soil remediation. One of the flavours of phytoremediation is rhizoremediation, where plant roots stimulate soil microbes to degrade organic contaminants. This approach is particularly interesting as it takes advantage of naturally evolved interaction mechanisms between plant and microorganisms and often results in a complete mineralization of the contaminants (i.e. transformation to water and CO2 ). However, many biotic and abiotic factors influence the outcome of this interaction, resulting in variable efficiency of the remediation process. The difficulty to predict precisely the timeframe associated with rhizoremediation leads to low adoption rates of this green technology. Here, we review recent literature related to rhizoremediation, with a particular focus on soil organisms. We then expand on the potential of rhizoremediation to be a model plant-microbe interaction system for microbiome manipulation studies.

The Sycamore Maple Bacterial Culture Collection From a TNT Polluted Site Shows Novel Plant-Growth Promoting and Explosives Degrading Bacteria

Military activities have worldwide introduced toxic explosives into the environment with considerable effects on soil and plant-associated microbiota. Fortunately, these microorganisms, and their collective metabolic activities, can be harnessed for site restoration via in situ phytoremediation. We characterized the bacterial communities inhabiting the bulk soil and rhizosphere of sycamore maple (Acer pseudoplatanus) in two chronically 2,4,6-trinitrotoluene (TNT) polluted soils. Three hundred strains were isolated, purified and characterized, a majority of which showed multiple plant growth promoting (PGP) traits. Several isolates showed high nitroreductase enzyme activity and concurrent TNT-transformation. A 12-member bacterial consortium, comprising selected TNT-detoxifying and rhizobacterial strains, significantly enhanced TNT removal from soil compared to non-inoculated plants, increased root and shoot weight, and the plants were less stressed than the un-inoculated plants as estimated by the responses of antioxidative enzymes. The sycamore maple tree (SYCAM) culture collection is a significant resource of plant-associated strains with multiple PGP and catalytic properties, available for further genetic and phenotypic discovery and use in field applications.

The rhizosphere microbiome: Significance in rhizoremediation of polyaromatic hydrocarbon contaminated soil

Microbial communities are an essential part of plant rhizosphere and participate in the functioning of plants, including rhizoremediation of petroleum contaminants. Rhizoremediation is a promising technology for removal of polyaromatic hydrocarbons based on interactions between plants and microbiome in the rhizosphere. Root exudation in the rhizosphere provides better nutrient uptake for rhizosphere microbiome, and therefore it is considered to be one of the major factors of microbial community function in the rhizosphere that plays a key role in the enhanced PAH biodegradation. Although the importance of the rhizosphere microbiome for plant growth has been widely recognized, the interactions between microbiome and plant roots in the process of rhizosphere mediated remediation of PAH still needs attention. Most of the current researches target PAH degradation by plant or single microorganism, separately, whereas the interactions between plants and whole microbiome are overlooked and its role has been ignored. This review summarizes recent knowledge of PAH degradation in the rhizosphere in the process of plant-microbiome interactions based on emerging omics approaches such as metagenomics, metatranscriptomics, metabolomics and metaproteomics. These omics approaches with combinations to bioinformatics tools provide us a better understanding in integrated activity patterns between plants and rhizosphere microbes, and insight into the biochemical and molecular modification of the meta-organisms (plant-microbiome) to maximize rhizoremediation activity. Moreover, a better understanding of the interactions could lead to the development of techniques to engineer rhizosphere microbiome for better hydrocarbon degradation.

Cadmium Exposure-Sedum alfredii Planting Interactions Shape the Bacterial Community in the Hyperaccumulator Plant Rhizosphere

Rhizospheric bacteria play important roles in plant tolerance and activation of heavy metals. Understanding the bacterial rhizobiome of hyperaccumulators may contribute to the development of optimized phytoextraction for metal-polluted soils. We used 16S rRNA gene amplicon sequencing to investigate the rhizospheric bacterial communities of the cadmium (Cd) hyperaccumulating ecotype (HE) Sedum alfredii in comparison to its nonhyperaccumulating ecotype (NHE). Both planting of two ecotypes of S. alfredii and elevated Cd levels significantly decreased bacterial alpha-diversity and altered bacterial community structure in soils. The HE rhizosphere harbored a unique bacterial community differing from those in its bulk soil and NHE counterparts. Several key taxa from Actinobacteria, Bacteroidetes, and TM7 were especially abundant in HE rhizospheres under high Cd stress. The actinobacterial genus Streptomyces was responsible for the majority of the divergence of bacterial community composition between the HE rhizosphere and other soil samples. In the HE rhizosphere, the abundance of Streptomyces was 3.31- to 16.45-fold higher than that in other samples under high Cd stress. These results suggested that both the presence of the hyperaccumulator S. alfredii and Cd exposure select for a specialized rhizosphere bacterial community during phytoextraction of Cd-contaminated soils and that key taxa, such as the species affiliated with the genus Streptomyces, may play an important role in metal hyperaccumulation.IMPORTANCESedum alfredii is a well-known Cd hyperaccumulator native to China. Its potential for extracting Cd relies not only on its powerful uptake, translocation, and tolerance for Cd but also on processes underground (especially rhizosphere microbes) that facilitate root uptake and tolerance of the metal. In this study, a high-throughput sequencing approach was applied to gain insight into the soil-plant-microbe interactions that may influence Cd accumulation in the hyperaccumulator S. alfredii Here, we report the investigation of rhizosphere bacterial communities of S. alfredii in phytoremediation of different levels of Cd contamination in soils. Moreover, some key taxa in its rhizosphere identified in the study, such as the species affiliated with genus Streptomyces, may shed new light on the involvement of bacteria in phytoextraction of contaminated soils and provide new materials for phytoremediation optimization.

Comparative Metatranscriptomics of Wheat Rhizosphere Microbiomes in Disease Suppressive and Non-suppressive Soils for Rhizoctonia solani AG8

The soilborne fungus Rhizoctonia solani anastomosis group (AG) 8 is a major pathogen of grain crops resulting in substantial production losses. In the absence of resistant cultivars of wheat or barley, a sustainable and enduring method for disease control may lie in the enhancement of biological disease suppression. Evidence of effective biological control of R. solani AG8 through disease suppression has been well documented at our study site in Avon, South Australia. A comparative metatranscriptomic approach was applied to assess the taxonomic and functional characteristics of the rhizosphere microbiome of wheat plants grown in adjacent fields which are suppressive and non-suppressive to the plant pathogen R. solani AG8. Analysis of 12 rhizosphere metatranscriptomes (six per field) was undertaken using two bioinformatic approaches involving unassembled and assembled reads. Differential expression analysis showed the dominant taxa in the rhizosphere based on mRNA annotation were Arthrobacter spp. and Pseudomonas spp. for non-suppressive samples and Stenotrophomonas spp. and Buttiauxella spp. for the suppressive samples. The assembled metatranscriptome analysis identified more differentially expressed genes than the unassembled analysis in the comparison of suppressive and non-suppressive samples. Suppressive samples showed greater expression of a polyketide cyclase, a terpenoid biosynthesis backbone gene (dxs) and many cold shock proteins (csp). Non-suppressive samples were characterised by greater expression of antibiotic genes such as non-heme chloroperoxidase (cpo) which is involved in pyrrolnitrin synthesis, and phenazine biosynthesis family protein F (phzF) and its transcriptional activator protein (phzR). A large number of genes involved in detoxifying reactive oxygen species (ROS) and superoxide radicals (sod, cat, ahp, bcp, gpx1, trx) were also expressed in the non-suppressive rhizosphere samples most likely in response to the infection of wheat roots by R. solani AG8. Together these results provide new insight into microbial gene expression in the rhizosphere of wheat in soils suppressive and non-suppressive to R. solani AG8. The approach taken and the genes involved in these functions provide direction for future studies to determine more precisely the molecular interplay of plant-microbe-pathogen interactions with the ultimate goal of the development of management options that promote beneficial rhizosphere microflora to reduce R. solani AG8 infection of crops.

Interacting effect of diclofop-methyl on the rice rhizosphere microbiome and denitrification

A better knowledge of the intertwined effects of herbicides on plant physiology and microbiome as well as nutrient biogeochemical cycles are needed for environmental management. Here we studied the influence of herbicide diclofop-methyl (DM) on the rice root microbiome and its relationship with N cycle. To do so, we exposed rice seedlings to 100 μg/L DM and studied rhizosphere microbiota using MiSeq-pyrosequencing, root exudation by GC-MS, and denitrification activity by ¹⁵N isotope-tracing and qRT-PCR. The richness and diversity of rhizosphere microorganisms, significantly increased after DM exposure combined with an increase in root exudation of amino acids, sugars, and fatty acids. Transcription of denitrification-related gene and denitrification rate increased significantly in the rice rhizosphere. Our results suggest that DM strongly influenced the root exudation of bacteria nutrients, which affected root microbiome community and potentially influenced N cycle in rice rhizosphere.

The influence of heavy metals, polyaromatic hydrocarbons, and polychlorinated biphenyls pollution on the development of antibiotic resistance in soils

The minireview is devoted to the analysis of the influence of soil pollution with heavy metals, polyaromatic hydrocarbons (PAHs), and the polychlorinated biphenyls (PCBs) on the distribution of antibiotics resistance genes (ARGs) in soil microbiomes. It is shown that the best understanding of ARGs distribution process requires studying the influence of pollutants on this process in natural microbiocenoses. Heavy metals promote co-selection of genes determining resistance to them together with ARGs in the same mobile elements of a bacterial genome, but the majority of studies focus on agricultural soils enriched with ARGs originating from manure. Studying nonagricultural soils would clear mechanisms of ARGs transfer in natural and anthropogenically transformed environments and highlight the role of antibiotic-producing bacteria. PAHs make a considerable shift in soil microbiomes leading to an increase in the number of Actinobacteria which are the source of antibiotics formation and bear multiple ARGs. The soils polluted with PAHs can be a selective medium for bacteria resistant to antibiotics, and the level of ARGs expression is much higher. PCBs are accumulated in soils and significantly alter the specific structure of soil microbiocenoses. In such soils, representatives of the genera Acinetobacter, Pseudomonas, and Alcanivorax dominate, and the ability to degrade PCBs is connected to horizontal gene transfer (HGT) and high level of genomic plasticity. The attention is also focused on the need to study the properties of the soil having an impact on the bioavailability of pollutants and, as a result, on resistome of soil microorganisms.

Enhanced phytoremdiation of Robinia pseudoacacia in heavy metal-contaminated soils with rhizobia and the associated bacterial community structure and function

Heavy metals can cause serious contamination of soils, especially in mining regions. A detailed understanding of the effects of heavy metals on plants and root-associated microbial communities could help to improve phytoremediation systems. In this study, black locust (Robinia pseudoacacia) seedlings with or without rhizobial inoculation were planted in soils contaminated with different levels of heavy metals. Bacterial communities in rhizosphere and bulk soil samples were analyzed using 16S rRNA gene sequencing on the Illumina MiSeq platform and shotgun metagenome sequencing on the Illumina HiSeq platform. Soil bacterial communities varied significantly depending on the level of soil contamination, and planting also had some influence. Although inoculation of Mesorhizobium loti HZ76 (a natural microsymbiont of R. pseudoacacia) was a relatively minor factor, it did influence the soil bacterial community. Under the selective pressure, plant growth promotion-related biomarkers in the rhizosphere increased after inoculation compared with non-inoculated controls, especially those associated with Mesorhizobium, Variovorax, Streptomyces, and Rhodococcus genera. Genes encoding ATP-binding cassette transporters were up-regulated in the rhizosphere after inoculation compared with genes related to sulfur/nitrogen metabolism. These results provide insight into soil bacterial communities and their functions in the R. pseudoacacia rhizosphere in response to rhizobial inoculation and heavy metal contamination. This knowledge may prove useful for improving phytoremediation of metal-contaminated soils.

Rhizosphere Microbiome Modulators: Contributions of Nitrogen Fixing Bacteria towards Sustainable Agriculture

Rhizosphere microbiome which has been shown to enhance plant growth and yield are modulated or influenced by a few environmental factors such as soil type, plant cultivar, climate change and anthropogenic activities. In particular, anthropogenic activity, such as the use of nitrogen-based chemical fertilizers, is associated with environmental destruction and this calls for a more ecofriendly strategy to increase nitrogen levels in agricultural land. This feat is attainable by harnessing nitrogen-fixing endophytic and free-living rhizobacteria. Rhizobium, Pseudomonas, Azospirillum and Bacillus, have been found to have positive impacts on crops by enhancing both above and belowground biomass and could therefore play positive roles in achieving sustainable agriculture outcomes. Thus, it is necessary to study this rhizosphere microbiome with more sophisticated culture-independent techniques such as next generation sequencing (NGS) with the prospect of discovering novel bacteria with plant growth promoting traits. This review is therefore aimed at discussing factors that can modulate rhizosphere microbiome with focus on the contributions of nitrogen fixing bacteria towards sustainable agricultural development and the techniques that can be used for their study.

Investigation of Rhizospheric Microbial Communities in Wheat, Barley, and Two Rice Varieties at the Seedling Stage

The plant rhizosphere microbiota plays multiple roles in plant growth. We investigated the taxonomic and functional variations in the rhizosphere microbial community, examining both prokaryotes and eukaryotes, of four crops at the seedling stage: wheat, barley, and two rice varieties ( indica and japonica) seeded in paddy soil. The diversity of rhizosphere communities in these four species was determined. Results showed that wheat and barley had much stronger selection effects than rice for the rhizosphere microbial community. Functional metagenomic profiling indicated that a series of sequences related to glycan, limonene, and pinene degradation pathways as well as some relatively rare functions related to N or S metabolism were enriched in the rhizosphere soil. We conclude that the four tested crops induced the formation of the microbial community with specific features that may influence the plant growth but stochastic processes also appreciably influenced the functional selection.

Trees, fungi and bacteria: tripartite metatranscriptomics of a root microbiome responding to soil contamination

BACKGROUND

One method for rejuvenating land polluted with anthropogenic contaminants is through phytoremediation, the reclamation of land through the cultivation of specific crops. The capacity for phytoremediation crops, such as Salix spp., to tolerate and even flourish in contaminated soils relies on a highly complex and predominantly cryptic interacting community of microbial life.

METHODS

Here, Illumina HiSeq 2500 sequencing and de novo transcriptome assembly were used to observe gene expression in washed Salix purpurea cv. 'Fish Creek' roots from trees pot grown in petroleum hydrocarbon-contaminated or non-contaminated soil. All 189,849 assembled contigs were annotated without a priori assumption as to sequence origin and differential expression was assessed.

RESULTS

The 839 contigs differentially expressed (DE) and annotated from S. purpurea revealed substantial increases in transcripts encoding abiotic stress response equipment, such as glutathione S-transferases, in roots of contaminated trees as well as the hallmarks of fungal interaction, such as SWEET2 (Sugars Will Eventually Be Exported Transporter). A total of 8252 DE transcripts were fungal in origin, with contamination conditions resulting in a community shift from Ascomycota to Basidiomycota genera. In response to contamination, 1745 Basidiomycota transcripts increased in abundance (the majority uniquely expressed in contaminated soil) including major monosaccharide transporter MST1, primary cell wall and lamella CAZy enzymes, and an ectomycorrhiza-upregulated exo-β-1,3-glucanase (GH5). Additionally, 639 DE polycistronic transcripts from an uncharacterised Enterobacteriaceae species were uniformly in higher abundance in contamination conditions and comprised a wide spectrum of genes cryptic under laboratory conditions but considered putatively involved in eukaryotic interaction, biofilm formation and dioxygenase hydrocarbon degradation.

CONCLUSIONS

Fungal gene expression, representing the majority of contigs assembled, suggests out-competition of white rot Ascomycota genera (dominated by Pyronema), a sometimes ectomycorrhizal (ECM) Ascomycota (Tuber) and ECM Basidiomycota (Hebeloma) by a poorly characterised putative ECM Basidiomycota due to contamination. Root and fungal expression involved transcripts encoding carbohydrate/amino acid (C/N) dialogue whereas bacterial gene expression included the apparatus necessary for biofilm interaction and direct reduction of contamination stress, a potential bacterial currency for a role in tripartite mutualism. Unmistakable within the metatranscriptome is the degree to which the landscape of rhizospheric biology, particularly the important but predominantly uncharacterised fungal genetics, is yet to be discovered.

Soil contamination alters the willow root and rhizosphere metatranscriptome and the root-rhizosphere interactome

Phytoremediation using willows is thought to be a sustainable alternative to traditional remediation techniques involving excavation, transport, and landfilling. However, the complexity of the interaction between the willow and its associated highly diverse microbial communities makes the optimization of phytoremediation very difficult. Here, we have sequenced the rhizosphere metatranscriptome of four willow species and the plant root metatranscriptome for two willow species growing in petroleum hydrocarbon-contaminated and non-contaminated soils on a former petroleum refinery site. Significant differences in the abundance of transcripts related to different bacterial and fungal taxa were observed between willow species, mostly in contaminated soils. When comparing transcript abundance in contaminated vs. non-contaminated soil for each willow species individually, transcripts for many microbial taxa and functions were significantly more abundant in contaminated rhizosphere soil for Salix eriocephala, S. miyabeana and S. purpurea, in contrast to what was observed in the rhizosphere of S. caprea. This agrees with the previously reported sensitivity of S. caprea to contamination, and the superior tolerance of S. miyabeana and S. purpurea to soil contamination at that site. The root metatranscriptomes of two species were compared and revealed that plants transcripts are mainly influenced by willow species, while microbial transcripts mainly responded to contamination. A comparison of the rhizosphere and root metatranscriptomes in the S. purpurea species revealed a complete reorganization of the linkages between root and rhizosphere pathways when comparing willows growing in contaminated and non-contaminated soils, mainly because of large shifts in the rhizosphere metatranscriptome.

Competitive Traits Are More Important than Stress-Tolerance Traits in a Cadmium-Contaminated Rhizosphere: A Role for Trait Theory in Microbial Ecology

Understanding how biotic and abiotic factors govern the assembly of rhizosphere-microbial communities is a long-standing goal in microbial ecology. In phytoremediation research, where plants are used to remediate heavy metal-contaminated soils, a deeper understanding of rhizosphere-microbial ecology is needed to fully exploit the potential of microbial-assisted phytoremediation. This study investigated whether Grime's competitor/stress-tolerator/ruderal (CSR) theory could be used to describe the impact of cadmium (Cd) and the presence of a Cd-accumulating plant, Carpobrotus rossii (Haw.) Schwantes, on the assembly of soil-bacterial communities using Illumina 16S rRNA profiling and the predictive metagenomic-profiling program, PICRUSt. Using predictions based on CSR theory, we hypothesized that Cd and the presence of a rhizosphere would affect community assembly. We predicted that the additional resource availability in the rhizosphere would enrich for competitive life strategists, while the presence of Cd would select for stress-tolerators. Traits identified as competitive followed CSR predictions, discriminating between rhizosphere and bulk-soil communities whilst stress-tolerance traits increased with Cd dose, but only in bulk-soil communities. These findings suggest that a bacterium's competitive attributes are critical to its ability to occupy and proliferate in a Cd-contaminated rhizosphere. Ruderal traits, which relate to community re-colonization potential, were synergistically decreased by the presence of the rhizosphere and Cd dose. Taken together this microcosm study suggests that the CSR theory is broadly applicable to microbial communities. Further work toward developing a simplified and robust strategy for microbial CSR classification will provide an ecologically meaningful framework to interpret community-level changes across a range of biomes.

Seed Endophyte Microbiome of Crotalaria pumila Unpeeled: Identification of Plant-Beneficial Methylobacteria

Metal contaminated soils are increasing worldwide. Metal-tolerant plants growing on metalliferous soils are fascinating genetic and microbial resources. Seeds can vertically transmit endophytic microorganisms that can assist next generations to cope with environmental stresses, through yet poorly understood mechanisms. The aims of this study were to identify the core seed endophyte microbiome of the pioneer metallophyte Crotalaria pumila throughout three generations, and to better understand the plant colonisation of the seed endophyte Methylobacterium sp. Cp3. Strain Cp3 was detected in C. pumila seeds across three successive generations and showed the most dominant community member. When inoculated in the soil at the time of flowering, strain Cp3 migrated from soil to seeds. Using confocal microscopy, Cp3-mCherry was demonstrated to colonise the root cortex cells and xylem vessels of the stem under metal stress. Moreover, strain Cp3 showed genetic and in planta potential to promote seed germination and seedling development. We revealed, for the first time, that the seed microbiome of a pioneer plant growing in its natural environment, and the colonisation behaviour of an important plant growth promoting systemic seed endophyte. Future characterization of seed microbiota will lead to a better understanding of their functional contribution and the potential use for seed-fortification applications.

Challenges and Approaches in Microbiome Research: From Fundamental to Applied

We face major agricultural challenges that remain a threat for global food security. Soil microbes harbor enormous potentials to provide sustainable and economically favorable solutions that could introduce novel approaches to improve agricultural practices and, hence, crop productivity. In this review we give an overview regarding the current state-of-the-art of microbiome research by discussing new technologies and approaches. We also provide insights into fundamental microbiome research that aim to provide a deeper understanding of the dynamics within microbial communities, as well as their interactions with different plant hosts and the environment. We aim to connect all these approaches with potential applications and reflect how we can use microbial communities in modern agricultural systems to realize a more customized and sustainable use of valuable resources (e.g., soil).

Rhizosphere effect is stronger than PAH concentration on shaping spatial bacterial assemblages along centimetre-scale depth gradients

At centimetre scale, soil bacterial assemblages are shaped by both abiotic (edaphic characteristics and pollutants) and biotic parameters. In a rhizobox experiment carried out on planted industrial soil contaminated with polycyclic aromatic hydrocarbons (PAHs), we previously showed that pollution was distributed randomly with hot and cold spots. Therefore, in the present study, we investigated the effect of this patchy PAH distribution on the bacterial community assemblage and compared it with that of root depth gradients found in the rhizosphere of either alfalfa or ryegrass. Sequencing of 16S rRNA amplicons revealed a higher bacterial diversity in ryegrass rhizosphere and enrichment in specific taxa by the 2 plant species. Indeed, Bacteroidetes, Firmicutes, and Gammaproteobacteria were globally favored in alfalfa, whereas Acidimicrobiia, Chloroflexi, Alpha-, and Betaproteobacteria were globally favored in ryegrass rhizosphere. The presence of alfalfa created depth gradients of root biomass, carbohydrate, and pH, and actually shaped the bacterial assemblage, favoring Actinobacteria near the surface and Gemmatimonadetes and Proteobacteria at greater depths. Contrarily, the bacterial assemblage was homogeneous all along depths of the ryegrass root system. With both plant species, the PAH content and random distribution had no significant effect on bacterial assemblage. Globally, at centimeter scale, bacterial community assemblages were mostly shaped by soil physical and chemical depth gradients induced by root growth but not by patchy PAH content.

Petroleum Contamination and Plant Identity Influence Soil and Root Microbial Communities While AMF Spores Retrieved from the Same Plants Possess Markedly Different Communities

Phytoremediation is a promising in situ green technology based on the use of plants to cleanup soils from organic and inorganic pollutants. Microbes, particularly bacteria and fungi, that closely interact with plant roots play key roles in phytoremediation processes. In polluted soils, the root-associated microbes contribute to alleviation of plant stress, improve nutrient uptake and may either degrade or sequester a large range of soil pollutants. Therefore, improving the efficiency of phytoremediation requires a thorough knowledge of the microbial diversity living in the rhizosphere and in close association with plant roots in both the surface and the endosphere. This study aims to assess fungal ITS and bacterial 16S rRNA gene diversity using high-throughput sequencing in rhizospheric soils and roots of three plant species (Solidago canadensis, Populus balsamifera, and Lycopus europaeus) growing spontaneously in three petroleum hydrocarbon polluted sedimentation basins. Microbial community structures of rhizospheric soils and roots were compared with those of microbes associated with arbuscular mycorrhizal fungal (AMF) spores to determine the links between the root and rhizosphere communities and those associated with AMF. Our results showed a difference in OTU richness and community structure composition between soils and roots for both bacteria and fungi. We found that petroleum hydrocarbon pollutant (PHP) concentrations have a significant effect on fungal and bacterial community structures in both soils and roots, whereas plant species identity showed a significant effect only on the roots for bacteria and fungi. Our results also showed that the community composition of bacteria and fungi in soil and roots varied from those associated with AMF spores harvested from the same plants. This let us to speculate that in petroleum hydrocarbon contaminated soils, AMF may release chemical compounds by which they recruit beneficial microbes to tolerate or degrade the PHPs present in the soil.