Assembly of root-associated microbiomes of typical rice cultivars in response to lindane pollution

A review of the impact of herbicides and insecticides on the microbial communities

Enhancing crop yield to accommodate the ever-increasing world population has become critical, and diminishing arable land has pressured current agricultural practices. Intensive farming methods have been using more pesticides and insecticides (biocides), culminating in soil deposition, negatively impacting the microbiome. Hence, a deeper understanding of the interaction and impact of pesticides and insecticides on microbial communities is required for the scientific community. This review highlights the recent findings concerning the possible impacts of biocides on various soil microorganisms and their diversity. This review's bibliometric analysis emphasised the recent developments' statistics based on the Scopus document search. Pesticides and insecticides are reported to degrade microbes' structure, cellular processes, and distinct biochemical reactions at cellular and biochemical levels. Several biocides disrupt the relationship between plants and their microbial symbionts, hindering beneficial biological activities that are widely discussed. Most microbial target sites of or receptors are biomolecules, and biocides bind with the receptor through a ligand-based mechanism. The biomarker action mechanism in response to biocides relies on activating the receptor site by specific biochemical interactions. The production of electrophilic or nucleophilic species, free radicals, and redox-reactive agents are the significant factors of biocide's metabolic reaction. Most studies considered for the review reported the negative impact of biocides on the soil microbial community; hence, technological development is required regarding eco-friendly pesticide and insecticide, which has less or no impact on the soil microbial community.

Residual effects of chlorinated organic pollutants on microbial community and natural redox processes in coastal wetlands

Chlorinated organic pollutants (COPs) are common in flooded environments. To examine the residual status and effects of COPs on flooded environments, a survey of 7 coastal wetlands in Zhejiang, East China was conducted. Total COP concentrations detected from 95.69 to 412.76 ng g-1 dw. Gamma-HCH and o,p'-DDT posed the greatest risk with exceedance rates of 100% according to sediment quality guidelines. Samples with higher COP pollution had higher microbial diversity, more complex microbial networks, more deterministic community assembly processes and lower microbiome stability, indicating an improved soil function for balance cycle of substances, especially for COP degradation. Further analysis using quantitative real-time PCR suggested COP-dechlorination interacted with natural redox processes, especially sulfate reduction and methanogenesis. The positive correlation between CH4 and pentachlorobenzene indicated a potential increase in greenhouse gas emissions caused by COP pollution. Correlation between dsr gene and COPs demonstrated the ability of sulfate-reducing bacteria to degrade COPs. Particularly, facultative OHRB such as sulfate-reducing bacteria hold significant importance in the process of COP-dechlorination. This finding provides a reference for COP pollution remediation. Collectively, our study offers new insight into the residual effect of COPs in coastal wetlands and contributes to an improved understanding of bioremediation strategies for COP pollution.

Response and adaptation of rhizosphere microbiome to organic pollutants with enriching pollutant-degraders and genes for bioremediation: A critical review

Phytoremediation largely involves microbial degradation of organic pollutants in rhizosphere for removing organic pollutants like polycyclic aromatic hydrocarbons, phthalates and polychlorinated biphenyls. Microbial community in rhizosphere experiences complex processes of response-adaptation-feedback up on exposure to organic pollutants. This review summarizes recent research on the response and adaptation of rhizosphere microbial community to the stress of organic pollutants, and discusses the enrichment of the pollutant-degrading microbial community and genes in the rhizosphere for promoting bioremediation. Soil pollution by organic contaminants often reduces the diversity of rhizosphere microbial community, and changes its functions. Responses vary among rhizosphere microbiomes up on different classes of organic pollutants (including co-contamination with heavy metals), plant species, root-associated niches (e.g., rhizosphere, rhizoplane and endosphere), geographical location and soil properties. Soil pollution can deplete some sensitive microbial taxa and enrich some tolerant microbial taxa in rhizosphere. Furthermore, rhizosphere enriches pollutant-degrading microbial community and functional genes including different gene clusters responsible for biodegradation of organic pollutants and their intermediates, which improve the adaptation of microbiome and enhance the remediation efficiency of the polluted soil. The knowledge gaps and future research challenges are highlighted on rhizosphere microbiome in response-adaptation-feedback processes to organic pollution and rhizoremediation. This review will hopefully update understanding on response-adaptation-feedback processes of rhizosphere microbiomes and rhizoremediation for the soil with organic pollutants.

The abundance of comammox bacteria was higher than that of ammonia-oxidizing archaea and bacteria in rhizosphere of emergent macrophytes in a typical shallow lake riparian

Complete ammonia oxidation (comammox) bacteria can complete the whole nitrification process independently, which not only challenges the classical two-step nitrification theory but also updates long-held perspective of microbial ecological relationship in nitrification process. Although comammox bacteria have been found in many ecosystems in recent years, there is still a lack of research on the comammox process in rhizosphere of emergent macrophytes in lakeshore zone. Sediment samples were collected in this study from rhizosphere, far-rhizosphere, and non-rhizosphere of emergent macrophytes along the shore of Lake Liangzi, a shallow lake. The diversity of comammox bacteria and amoA gene abundance of comammox bacteria, ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB) in these samples were measured. The results showed that comammox bacteria widely existed in the rhizosphere of emergent macrophytes and fell into clade A.1, clade A.2, and clade B, and clade A was the predominant community in all sampling sites. The abundance of comammox amoA gene (6.52 × 106-2.45 × 108 copies g-1 dry sediment) was higher than that of AOB amoA gene (6.58 × 104-3.58 × 106 copies g-1 dry sediment), and four orders of magnitude higher than that of AOA amoA gene (7.24 × 102-6.89 × 103 copies g-1 dry sediment), suggesting that the rhizosphere of emergent macrophytes is more favorable for the growth of comammox bacteria than that of AOB and AOA. Our study indicated that the comammox bacteria may play important roles in ammonia-oxidizing processes in all different rhizosphere regions.

Research progress on remediation of organochlorine pesticide contamination in soil

Deteriorated soil pollution has grown into a worldwide environmental concern over the years. Organochlorine pesticide (OCP) residues, featured with ubiquity, persistence and refractoriness, are one of the main pollution sources, causing soil degradation, fertility decline and nutritional imbalance, and severely impacting soil ecology. Furthermore, residual OCPs in soil may enter the human body along with food chain accumulation and pose a serious health threat. To date, many remediation technologies including physicochemical and biological ways for organochlorine pollution have been developed at home and abroad, but none of them is a panacea suitable for all occasions. Rational selection and scientific decision-making are grounded in in-depth knowledge of various restoration techniques. However, soil pollution treatment often encounters the interference of multiple factors (climate, soil properties, cost, restoration efficiency, etc.) in complex environments, and there is still a lack of systematic summary and comparative analysis of different soil OCP removal methods. Thus, to better guide the remediation of contaminated soil, this review summarized the most commonly used strategies for OCP removal, evaluated their merits and limitations and discussed the application scenarios of different methods. It will facilitate the development of efficient, inexpensive and environmentally friendly soil remediation strategies for sustainable agricultural and ecological development.

Integrating compound-specific stable isotope and enantiomer-specific analysis to characterize the isomeric and enantiomeric signatures of hexachlorocyclohexanes (HCHs) in paddy soils

Organic pollutants in paddy fields may undergo different processes from those in dryland due to the anaerobic environment. The integrated use of compound-specific stable isotope analysis (CSIA) and enantiomer-specific analysis is a promising technique for understanding the behavior and fate of organic pollutants in soils. In this study, soil samples were collected from paddy fields in three major rice cultivation regions of China, spanning a transect of 4000 km. The mean concentrations of ƩHCHs in paddy soils from the Taihu Plain were the highest (1.44 ng/g). The ratios of α-HCH/β-HCH (all below 11.8) and α-HCH/γ-HCH (92% below 4.64), as well as the enantiomeric fractions (EFs) of chiral α-HCH (mean of 0.81), reflected that the distribution of HCHs was affected by the use of both technical HCHs and lindane. The preferential depletion of (-)-α-HCH and pronounced carbon isotope fractionation of α-HCH (δ13C of -28.22 ± 0.92‰ -23.63 ± 1.89‰) demonstrated its effective transformation. Factors such as altitude, soil temperature, soil pH, soil conductivity and soil organic matter significantly influenced the fate and transformation of HCHs. The current study highlights the integrated application of CSIA and enantiomer-specific analysis to provide multiple lines of evidence for the transformation of HCHs in soils.

Rice genotypes and root-associated niches shifted bacterial community in response to pollution of di-(2-ethylhexyl) phthalate (DEHP) for promoting DEHP removal

Organic pollutants influenced root-associated bacterial community. However, the response variation of root-associated bacterial community among different rice genotypes exposed to phthalates (PAEs) and their removal mechanism remains unknown. Here, bacterial community and PAE-degrading genes in root-associated niches were analyzed between low (Fengyousimiao) and high (Hhang) PAE-accumulating rice cultivars exposed to di-(2-ethylhexyl) phthalate (DEHP). DEHP dissipation percentages in rhizosphere of Hhang were significantly higher than those of Fengyousimiao. The bacterial community diversities (including Chao1 and Shannon index) significantly decreased along bulk soil - rhizosphere - rhizoplane - endosphere. The bacterial community structures were shaped mainly by root-associated niches, DEHP pollution and rice genotypes, with significant differences in rhizosphere and rhizoplane between Fengyousimiao and Hhang. Rhizosphere enriched more PAE-degrading bacteria than in bulk soil, and exhibited significantly higher expression of PAE-degrading genes (hydrolase 65, phtab, phtC, pcaF and pcaI) than in bulk soil. Furthermore, rhizosphere of Hhang demonstrated significantly stronger bacterial functions related to xenobiotics biodegradation and higher expression of PAE-degrading genes than those of Fengyousimiao, leading to significantly higher DEHP dissipation percentages in rhizosphere of Hhang. The findings demonstrate that Hhang shaped specific root-associated bacterial community with higher abundances of PAE-degrading bacteria and genes than Fengyousimiao to promote DEHP degradation.

Piriformospora indica alter root-associated microbiome structure to enhance Artemisia annua L. tolerance to arsenic

Microorganisms in the rhizosphere are crucial allies for plant stress tolerance. Recent research suggests that by interacting with the rhizosphere microbiome, microorganisms can aid in the revegetation of soils contaminated with heavy metal(loid)s (HMs). However, it is unknown that how Piriformospora indica influences the rhizosphere microbiome to mitigate arsenic-toxicity in arsenic-enriched environments. Artemisia annua plants were grown in the presence or absence of P. indica and spiked with low (50) and high (150 µmol/L) concentrations of arsenic (As). After inoculation with P. indica, fresh weight increased by 37.7% and 10% in control and high concentration treated plants, respectively. Transmission electron microscopy showed that cellular organelles were severely damaged by As and even disappeared under high concentration. Furthermore, As was mostly accumulated by 5.9 and 18.1 mg/kg dry weight in the roots of inoculated plants treated with low and high concentrations of As, respectively. Additionally, 16 S and ITS rRNA gene sequencing were applied to analyze the rhizosphere microbial community structure of A. annua under different treatments. A significant difference was observed in microbial community structure under different treatments as revealed by non-metric multidimensional scaling ordination. The bacterial and fungal richness and diversity in the rhizosphere of inoculated plants were actively balanced and regulated by P. indica co-cultivation. Lysobacter and Steroidobacter were found to be the As-resistant bacterial genera. We conclude that P. indica inoculation could alter rhizosphere microecology, thereby mitigating As-toxicity without harming the environment.

Iron plaque formation and its effect on key elements cycling in constructed wetlands: Functions and outlooks

Ecological restoration of wetland plants has emerged as an environmentally-friendly and less carbon footprint method for treating secondary effluent wastewater. Root iron plaque (IP) is located at the important ecological niches in constructed wetlands (CWs) ecosystem and is the critical micro-zone for pollutants migration and transformation. Root IP can affect the chemical behaviors and bioavailability of key elements (C, N, P) since its formation/dissolution is a dynamic equilibrium process jointly influenced by rhizosphere habitats. However, as an efficient approach to further explore the mechanism of pollutant removal in CWs, the dynamic formation of root IP and its function have not been fully studied, especially in substrate-enhanced CWs. This article concentrates on the biogeochemical processes between Fe cycling involved in root IP with carbon turnover, nitrogen transformation, and phosphorus availability in CWs rhizosphere. As IP has the potential to enhance pollutant removal by being regulated and managed, we summarized the critical factors affecting the IP formation from the perspective of wetland design and operation, as well as emphasizing the heterogeneity of rhizosphere redox and the role of key microbes in nutrient cycling. Subsequently, interactions between redox-controlled root IP and biogeochemical elements (C, N, P) are emphatically discussed. Additionally, the effects of IP on emerging contaminants and heavy metals in CWs rhizosphere are assessed. Finally, major challenges and outlooks for future research in regards to root IP are proposed. It is expected that this review can provide a new perspective for the efficient removal of target pollutants in CWs.

Potential risk of co-occurrence of microplastics and chlorinated persistent organic pollutants to coastal wetlands: Evidence from a case study

Microplastic (MP) pollution in coastal wetlands is of a global concern. Little attention has been paid to the co-occurrence and corresponding risk of MPs with pollutants, especially refractory chlorinated persistent organic pollutants (CPOPs). A case study of Zhejiang, China was conducted to investigate the occurrence of MPs and targeted CPOPs in coastal wetlands. MPs were 100% detected, but with the lowest abundance in coastal wetlands (average: 666.1 ± 159.1 items kg^-1), as compared to other 6 terrestrial ecosystems (average: 1293.9 ± 163.7 items kg^-1) including paddy field, upland, facility vegetable field, forestland, urban soil, and grassland. A total of 35 kinds CPOPs were also detected in all studied coastal wetlands, with their concentration almost under 10 μg kg^-1 (90.1%). Both enrichment of MPs and CPOPs was affected by sediment TOC, wetland vegetation and land use simultaneously. Interestingly, the occurrence of MPs was significantly correlated with polychlorinated biphenyls (PCBs) but not organochlorine pesticides (OCPs). Results of co-occurrence pollution assessment of MPs and CPOPs further indicated only Hangzhou Bay showed the ecological risk among all tested wetlands. This would suggest a potential risk of co-occurrence of MPs and modern CPOPs in coastal wetland in economic development area. Possible reason may lie on strong MP vector effect to CPOPs. More attention should thus be paid to other wetlands polluted by MPs and MP-carrying CPOPs in area with relatively great environmental pressure induced by human activity. This study may provide reference for a better understanding with respect to the risk level posed by co-occurrence of MPs and CPOPs to global coastal wetlands.

Metagenomic and machine learning-aided identification of biomarkers driving distinctive Cd accumulation features in the root-associated microbiome of two rice cultivars

Developing low-cadmium (Cd) rice cultivars has emerged as a promising avenue for food safety in Cd-contaminated farmlands. The root-associated microbiomes of rice have been shown to enhance rice growth and alleviate Cd stress. However, the microbial taxon-specific Cd resistance mechanisms underlying different Cd accumulation characteristics between different rice cultivars remain largely unknown. This study compared low-Cd cultivar XS14 and hybrid rice cultivar YY17 for Cd accumulation with five soil amendments. The results showed that XS14 was characterized by more variable community structures and stable co-occurrence networks in the soil-root continuum compared to YY17. The stronger stochastic processes in assembly of the XS14 (~25%) rhizosphere community than that of YY17 (~12%) suggested XS14 may have higher resistance to changes in soil properties. Microbial co-occurrence networks and machine learning models jointly identified keystone indicator microbiota, such as Desulfobacteria in XS14 and Nitrospiraceae in YY17. Meanwhile, genes involved in sulfur cycling and nitrogen cycling were observed among the root-associated microbiome of these two cultivars, respectively. Microbiomes in the rhizosphere and root of XS14 showed a higher diversity in functioning, with the significant enrichment of functional genes related to amino acid and carbohydrate transport and metabolism, and sulfur cycling. Our findings revealed differences and similarities in the microbial communities associated with two rice cultivars, as well as bacterial biomarkers predictive of Cd-accumulation capacity. Thus, we provide new insights into taxon-specific recruitment strategies of two rice cultivars under Cd stress and highlight the utility of biomarkers in offering clues for enhancing crop resilience to Cd stresses in the future.

Diversity-triggered bottom-up trophic interactions impair key soil functions under lindane pollution stress

A growing amount of evidence suggests that microbial diversity loss may have negative effects on soil ecosystem function. However, less attention has been paid to the determinants of the relationship between community diversity and soil functioning under pollution stress. Here we manipulated microbial diversity to observe how biotic and abiotic factors influenced soil multi-functions (e.g. lindane degradation, soil respiration and nutrient cycling). Results showed that protist community was more sensitive to dilution, pollution stress, and sodium acetate addition than bacterial and fungal community. Acetate addition accelerated the lindane removal. Any declines in microbial diversity reduced the specialized soil processes (NO₃-N production, and N₂O flux), but increased soil respiration rate. Dilution led to a significant increase in consumers-bacterial and fungi-bacterial interaction as evidenced by co-occurrence network, which possibly played roles in maintaining microbiome stability and resilience. Interestingly, pollution stress and resource availability weaken the relationship between microbial diversity and soil functions through the bottom-up trophic interaction and environmental preference of soil microbiome. Overall, this work provides experimental evidence that loss in microbial diversity, accompanied with changes in trophic interactions mediated biotic and abiotic factors, could have important consequences for specialized soil functioning in farmland ecosystems.

Different factors drive the assembly of pine and Panax notoginseng-associated microbiomes in Panax notoginseng-pine agroforestry systems

Land-use conversion affects the composition and assembly of plant-associated microbiomes, which in turn affects plant growth, development, and ecosystem functioning. However, agroforestry systems, as sustainable land types, have received little attention regarding the dynamics of different plant-associated microbes. In this study, we used high-throughput sequencing technology to analyze the assembly mechanisms and the driving factors of pine- and Panax notoginseng (P.n.)-associated microbiomes during the conversion of different pine forests (Pinus kesiya var. langbianensis and Pinus armandii) into P.n.-pine agroforestry systems. The results showed that the conversion of pure pine forest into P.n.-pine agroforestry systems significantly altered the diversity of pine-associated fungi rather than the community structure, and the community structure of P.n.-associated fungi rather than the diversity. Additionally, plant-associated fungi were more responsive to land-use change than bacteria. Main effect analysis revealed that compartment rather than genotype was the driving factor of pine- and P.n.-associated microbiomes, but P.n. cultivation also significantly affected the assembly of pine-associated microbiomes. In addition, there was a transfer of P.n. endophytes to pine trees in agroforestry systems and the beneficial microbiomes (Massilia, Marmoricola, Herbaspirillum, etc.) were enlarged in pine roots. Therefore, the diversity of the assembly mechanisms of P.n.- and pine-associated microbiomes played an important role in the P.n.--pine agroforestry systems and were the basis for the sustainable development of the P.n.--pine agroforestry systems.

DNA stable isotope probing on soil treated by plant biostimulation and flooding revealed the bacterial communities involved in PCB degradation

Polychlorinated biphenyl (PCB)-contaminated soils represent a major treat for ecosystems health. Plant biostimulation of autochthonous microbial PCB degraders is a way to restore polluted sites where traditional remediation techniques are not sustainable, though its success requires the understanding of site-specific plant-microbe interactions. In an historical PCB contaminated soil, we applied DNA stable isotope probing (SIP) using ¹³C-labeled 4-chlorobiphenyl (4-CB) and 16S rRNA MiSeq amplicon sequencing to determine how the structure of total and PCB-degrading bacterial populations were affected by different treatments: biostimulation with Phalaris arundinacea subjected (PhalRed) or not (Phal) to a redox cycle and the non-planted controls (Bulk and BulkRed). Phal soils hosted the most diverse community and plant biostimulation induced an enrichment of Actinobacteria. Mineralization of 4-CB in SIP microcosms varied between 10% in Bulk and 39% in PhalRed soil. The most abundant taxa deriving carbon from PCB were Betaproteobacteria and Actinobacteria. Comamonadaceae was the family most represented in Phal soils, Rhodocyclaceae and Nocardiaceae in non-planted soils. Planted soils subjected to redox cycle enriched PCB degraders affiliated to Pseudonocardiaceae, Micromonosporaceae and Nocardioidaceae. Overall, we demonstrated different responses of soil bacterial taxa to specific rhizoremediation treatments and we provided new insights into the populations active in PCB biodegradation.

Dynamic Fluctuation and Niche Differentiation of Fungal Pathogens Infecting Bell Pepper Plants

The plant microbiome is shaped by plant development and microbial interaction. Fungal pathogens infecting bell pepper plants may fluctuate across the growing seasons. Dynamic fluctuation of the microbiome and fungal pathogens in bell pepper plants is poorly understood, and the origin of fungal pathogens causing fruit rot and leaf wilt has been barely investigated. In this study, we used amplicon sequencing (i.e., 16S rRNA and internal transcribed spacer [ITS] sequencing) to explore the compositional variations of the microbiome in bell pepper plants and studied the fluctuation of fungal pathogens across the growing seasons. Co-occurrence network analysis was applied to track the origin and dissemination route of fungal pathogens that infected bell pepper plants. ITS and 16S rRNA sequencing analyses demonstrated that fungal pathogens infecting fruits and leaves probably belonged to the Penicillium, Cladosporium, Fusarium, and unclassified_Sclerotiniaceae genera rather than one specific genus. The dominant fungal pathogens were different, along with the development of bell pepper plants. Both plant development and fungal pathogens shaped microbial communities in bell pepper plants across the growing seasons. Fungal pathogens decreased species richness and diversity of fungal communities in fungus-infected fruit and leaf tissues but not the uninfected stem tissues. Bacterial metabolic functions of xenobiotics increased in fungus-infected leaves at a mature developmental stage. Competitive interaction was present between fungal and bacterial communities in leaves. Co-occurrence network analysis revealed that the origins of fungal pathogens included the greenhouse, packing house, and storage room. Niche differentiation of microbes was discovered among these locations. IMPORTANCE Bell peppers are widely consumed worldwide. Fungal pathogen infections of bell peppers lead to enormous economic loss. To control fungal pathogens and increase economic benefit, it is essential to investigate the shifting patterns of the microbiome and fungal pathogens in bell pepper plants across the growing seasons. In this study, bell pepper plant diseases observed in fruits and leaves were caused by different fungal pathogens. Fungal pathogens originated from the greenhouse, packing house, and storage room, and niche differentiation existed among microbes. This study improves the understanding of dynamic fluctuation and source of fungal pathogens infecting bell pepper plants in the farming system. It also facilitates precise management of fungal pathogens in the greenhouse.

Biochar alleviated the toxicity of atrazine to soybeans, as revealed by soil microbial community and the assembly process

Atrazine has a detrimental effect on soybean growth in corn-soybean rotation systems. A knowledge gap exists regarding how rhizosphere microbial interactions respond to atrazine stress, and specifically, whether they may alleviate the detriment of atrazine on soybeans, this serving as a target to alleviate the adverse impact. Biochar are widely used for remediation in herbicide contamination soil, however, little is known about how biochar fuels the microbiomes in rhizosphere to improve soybean performance. We investigated the response of the microbial community to atrazine stress with and without biochar application to soybean cultivation in a greenhouse experiment. Atrazine had detrimental effects on soybeans and nodules, reshaping the microbial community in both the bulk and rhizosphere soil. Biochar application was able to ameliorate atrazine effects on soybean and nodule activity, with an increase in competition among microbes in the soybean rhizosphere soils. Biochar favored the probiotics such as the bacteria Lysobacter, Paenarthrobacter, and Sediminibacterium in the rhizosphere soils. The relative abundance of Lysobacter exhibited strong-negative correlations with potential pathogens. Elastic net regression with bioindicators and environmental factors accurately predicted the residual content of atrazine in soil. Collectively, our results provide a practical strategy of using biochar to improve soil quality for corn-soybean rotation that is contaminated with residual atrazine. Overall, beneficial plant microbes and changes in microbial interactions and assembly processes in the soybean rhizosphere are capable of alleviating atrazine stress on soybean growth.

Community reassemblies of eukaryotes, prokaryotes, and viruses in the hexabromocyclododecanes-contaminated microcosms

The microbial community in seriously contaminated environment were not well known. This research investigated the community reassemblies in microcosms made of two distinct mangrove sediments amended with high levels of hexabromocyclododecanes (HBCDs). After eight months of contamination, the transformation of HBCDs yielded various lower brominated products and resulted in acidification (pH ~2). Therefore, the degraders and dehalogenase homologous genes involved in transformation of HBCDs only presented in low abundance to avoid further deterioration of the habitats. Moreover, in these deteriorated habitats, 1344 bacterial, 969 archaeal, 599 eukaryotic (excluded fungi), 187 fungal OTUs, and 10 viral genera, were reduced compared with controls. Specifically, in two groups of microcosms, Zetaproteobacteria, Deinococcus-Thermus, Spirochaetes, Bacteroidetes, Euryarchaeota, and Ascomycota, were positively responding taxa to HBCDs. Caloneis (Bacillariophyta) and Ascomycota turned to the dominant eukaryotic and fungal taxa. Most of predominant taxa were related to the contamination of brominated flame retardants (BFRs). Microbial communities were reassembled in divergent and sediment-dependent manner. The long-term contamination of HBCDs leaded to the change of relations between many taxa, included some of the environmental viruses and their known hosts. This research highlight the importance of monitoring the ecological effects around plants producing or processing halogenated compounds.

Diel Fluctuation of Extracellular Reactive Oxygen Species Production in the Rhizosphere of Rice

Reactive oxygen species (ROS) are ubiquitous on earth and drive numerous redox-centered biogeochemical processes. The rhizosphere of wetland plants is a highly dynamic interface for the exchange of oxygen and electrons, presenting the basis of the precedent for ROS production, yet whether extracellular ROS are produced in the rhizosphere remains unknown. Here, we designed a microfluidic chip setup to detect in-situ ROS productions in the rhizosphere of rice with spatial and temporal resolutions. Fluorescence imaging clearly displayed the hot spots of ROS generation in the rhizosphere. The formation concentration of the hydroxyl radical (^•OH, a representative ROS, 10^-6 M) was comparable to those by the classical photochemical route (10^-6-10^-7 M) in aquatic systems, therefore highlighting the rhizosphere as an unrecognized hotspot for ROS production. Moreover, the rhizosphere ROS production exhibits diel fluctuation, which simultaneously fluctuated with dissolved oxygen, redox potential, and pH, all driven by radial oxygen loss near the root in the daytime. The production and diel fluctuation of ROS were confirmed in the rhizosphere of rice root incubated in natural soils. We demonstrated that the extracellular ROS production was triggered by the interplay between root-released oxygen and microbial respiration released extracellular electrons, while iron mineral and organic matter might play key roles in storing and shuttling electrons. Our results highlight the rhizosphere as a widespread but previously unappreciated hotspot for ROS production, which may affect pollutant redox dynamics and biogeochemical processes in soils.

Maize root-associated niches determine the response variation in bacterial community assembly and function to phthalate pollution

Plant root-associated microbiome can be influenced by environmental stress like pollution. However, how organic pollution influences microbial communities in different root-associated niches and plant-microbe interaction remains unclear. We analyzed maize root-associated bacterial communities under stress of di-(2-ethylhexyl) phthalate (DEHP). The results demonstrate that structures and functions of bacterial communities are significantly different among four root-associated niches, and bacterial diversities gradually decline along bulk soil - rhizosphere - rhizoplane - endosphere. DEHP stress significantly reduces bacterial community diversities in both rhizosphere and rhizoplane, and changes their composition, enrichment and depleting process. DEHP stress led to the enrichment of some specific bacterial taxa like phthalate-degrading bacteria (e.g., Rhizobium and Agromyces) and functional genes involving in phthalate degradation (e.g., pht3 and pcaG). Notably, rhizoplane bacterial community is more sensitive to DEHP stress by enriching stress-resistant bacteria and more complex microbial network on rhizoplane than in rhizosphere. DEHP stress also disturbs the colonization and biofilm forming of root-associated bacteria on rhizoplane. Rhizoplane bacterial community is significantly correlated with maize growth while negatively influenced by DEHP stress. DEHP stress negatively influences plant-microbe interaction and inhibits maize growth. This study provides deep and comprehensive understanding for root-associated bacterial community in response to organic pollution.

Assembly of root-associated bacterial community in cadmium contaminated soil following five-year consecutive application of soil amendments: Evidences for improved soil health

Soil amendments have been extensively used to remediate heavy metal contaminated soils by immobilizing or altering edaphic properties to reduce the bioavailability of heavy metals. However, the potential influences of long-term soil amendments applications on microbial communities and polluted soil health are still in its infancy despite that have been applied for decades. We used amplicon sequencing and q-PCR array to characterize the root-associated microbial community compositions and rhizosphere functional genes in a five-year field experiment with consecutive application of four amendments (lime, biochar, pig manure, and a commercial Mg-Ca-Si conditioner). Compared with the control, soil amendments reduced the available Cd (CaCl₂ extractable Cd) in soils and strongly affected bacterial community compositions in four root-associated niches. Five rare keystone bacterial species were found belonging to the family Gallionellaceae (1), Haliangiaceae (1), Anaerolineaceae (2), and Xanthobacteraceae (1), which significantly correlated with soil pH and the functional genes nifH and phoD. Random forest analysis showed that rhizosphere soil pH and microbial functions, and root-associated keystone bacterial community compositions mainly influenced the Cd concentrations in rice grains. Altogether, our field data revealed five-year consecutive application of soil amendments regulated root-associated microbial community assembly and enhanced microbial functions, thereby improved rhizosphere health of Cd-contaminated soils.

Impact of hexachlorocyclohexane addition on the composition and potential functions of the bacterial community in red and purple paddy soil

Soil studies have reported the effect of Hexachlorocyclohexane (HCH) on soil microbial communities. However, how soil microbial communities and function shift after HCH addition into the red and purple soil remains unclear. Here, we analyzed the HCH residue fate, and the functional composition and structure of microbial communities to HCH in the two soils. Under the 100 g/ha and 1000 g/ha treatment, the dissipation rate of HCH was 0.0386 and 0.0273 in the purple soil, 0.0145 and 0.0195 in the red soil. The enrichment of HCH degrading genes leads to a higher HCH dissipation rate in the purple soil. PCoA results demonstrated that HCH addition has a different effect on the community diversity in the two soils, and Proteobacteria and Acidobacteria were the major phyla in the two soils. The soil microbiome average variation degree values of red soil were higher than purple soil, which indicated that the soil microbiome in the purple soil was more stable than in the red soil under HCH addition. PICRUSt2 results indicated that functional genes involved in the carbon, nitrogen biogeochemical cycles and HCH degradation were more tolerant to HCH addition in the purple soil. This study provides new insights into understanding of the effect of HCH addition on soil microbial communities and function in the red and purple paddy soil.

Impacts of earthworm casts on atrazine catabolism and bacterial community structure in laterite soil

Atrazine accumulation in agricultural soil is prone to cause serious environmental problems and pose risks to human health. Vermicomposting is an eco-friendly approach to accelerating atrazine biodegradation, but the roles of earthworm cast in the accelerated atrazine removal remains unclear. This work aimed to investigate the roles of earthworm cast in promoting atrazine degradation performance by comprehensively exploring the change in atrazine metabolites and bacterial communities. Our results showed that earthworm cast amendment significantly increased soil pH, organic matters, humic acid, fulvic acid and humin, and achieved a significantly higher atrazine removal efficiency. Earthworm cast addition also remarkably changed soil microbial communities by enriching potential soil atrazine degraders (Pseudomonadaceae, Streptomycetaceae, and Thermomonosporaceae) and introducing cast microbial degraders (Saccharimonadaceae). Particularly, earthworm casts increased the production of metabolites deethylatrazine and deisopropylatrazine, but not hydroxyatrazine. Some bacterial taxa (Gaiellaceaea and Micromonosporaceae) and humus (humic acid, fulvic acid and humin) were strongly correlated with atrazine metabolism into deisopropylatrazine and deethylatrazine, whereas hydroxyatrazine production was benefited by higher pH. Our findings verified the accelerated atrazine degradation with earthworm cast supplement, providing new insights into the influential factors on atrazine bioremediation in vermicomposting.

Light exposure mediates circadian rhythms of rhizosphere microbial communities

Microbial community circadian rhythms have a broad influence on host health and even though light-induced environmental fluctuations could regulate microbial communities, the contribution of light to the circadian rhythms of rhizosphere microbial communities has received little attention. To address this gap, we monitored diel changes in the microbial communities in rice (Oryza sativa L.) rhizosphere soil under light-dark and constant dark regimes, identifying microbes with circadian rhythms caused by light exposure and microbial circadian clocks, respectively. While rhizosphere microbial communities displayed circadian rhythms under light-dark and constant dark regimes, taxa possessing circadian rhythms under the two conditions were dissimilar. Light exposure concealed microbial circadian clocks as a regulatory driver, leading to fewer ecological niches in light versus dark communities. These findings disentangle regulation mechanisms for circadian rhythms in the rice rhizosphere microbial communities and highlight the role of light-induced regulation of rhizosphere microbial communities.

Histological effects of sublethal concentrations of insecticide Lindane on intestinal tissue of grass carp (Ctenopharyngodon idella)

This study investigates acute toxicity and histological effects of Lindane insecticide on intestinal tissues of immature grass carp (Ctenopharyngodon idella). For these purposes, 105 fish were exposed to different concentrations of Lindane for 96 h in 5 groups with 3 replications. Samples of intestinal tissues were prepared in both control and exposure groups during and after the toxicity test. Vaculation, necrosis, bleeding and epithelial degeneration were apparent in the intestine tissue of treated individuals. The LC₅₀ 96 h of Lindane was 0.788 ppm in the present study, also the results showed besides pesticide-induced lesions, symptoms of abnormal swimming, anxiety, tendency to swim near the surface, and death due to terminal toxicity with mouth widely open. The exposed fish were pale in color, showed oxygen deficit and severe respiratory problems. Overall, our results confirm the toxicity of different concentrations of Lindane insecticide affecting behavior, intestinal function and inducing tissue lesions of immature grass carp.

Microbial and abiotic factors of flooded soil that affect redox biodegradation of lindane

Pollution induces pressure to soil microorganism; and conversely, the degradation of pollutants is reported largely regulated by the soil microbiome assembly in situ. However, the specific-dependent core taxa of degraders were barely confirmed, which is not conducive to improving the soil remediation strategy. Taking pollution of a typical organochlorine pesticide (OCP), lindane, as an example, we explored the microbial community assembly in flooded soils and simultaneously quantified the corresponding dynamics of typical soil redox processes. Contrasting initial status of microbial diversity was set up by gamma irradiation or not, with additives (acetate, NaNO_3, acetate + NaNO₃) capable of modifying microbial growth employed simultaneously. Microorganism under lindane stress was reflected by microbial adaptability within complex co-occurrence networks, wherein some environment-dependent core taxa (e.g., Clostridia, Bacteroidia, Bacilli) were highly resilient to pollution and sterilization disturbances. Lindane had higher degradation rate in irradiated soil (0.96 mg kg^-1 d^-1) than non-irradiated soil (0.83 mg kg^-1 d^-1). In non-irradiated soil, addition of acetate promoted lindane degradation and methanogenesis, whereas nitrate inhibited lindane degradation but promoted denitrification. No significant differences in lindane degradation were observed in irradiated soils, which exhibited low-diversity microbiomes in parallel to stronger Fe reduction and methanogenesis. The varied corresponding trigger effects on soil redox processes are likely due to differences of soil microbiome, specifically, deterministic or stochastic assembly, in response to pollution stress under high or low initial microbial diversity conditions. Our results improve the knowledge of the adaptability of disturbed microbiomes and their feedback on microbial functional development in OCP-polluted soils, achieving for a more reliable understanding with respect to the ecological risk of soils resided with OCPs under the fact of global microbial diversity loss.

Assembly strategies of the wheat root-associated microbiome in soils contaminated with phenanthrene and copper

Plants can cope with stressful conditions by indirectly regulating root-associated microbial structures. However, the recruitment strategies of the root-associated microbiome in combined organic and inorganic contaminated soils are not well known, especially for common agricultural crops. In this study, we performed greenhouse experiments to investigate the interactive effects of joint copper (Cu) and phenanthrene (PHE) pollution on wheat growth and microbial detoxication processes. Results show that heavy metals did not affect PHE dissipation in the rhizosphere but significantly enhanced the accumulation of PHE in the endosphere. In contrast, the addition of PHE did not influence the absorption of Cu by wheat roots. Cu was the primary factor affecting the variation of microbial communities in cocontaminated treatments among each rhizocompartment while the interactive effects of combined pollutants were only detected in unplanted bulk soil. Microbes are known to degrade polycyclic aromatic hydrocarbons and tolerant heavy metal stress e.g. Novosphingobium, Sphingomonas, Sphingobium and Pseudomonas enriched in the contaminated treatments. Our results provide an integrated understanding of the synthetic effects of combined pollutants on the root-microbial assemblage process in plant-soil systems and offer useful information on the selection of effective bioremediating root-associated microbes for the application of self-remediation by common crops.

Potential Role of Methanogens in Microbial Reductive Dechlorination of Organic Chlorinated Pollutants In Situ

Previous studies often attribute microbial reductive dechlorination to organohalide-respiring bacteria (OHRB) or cometabolic dechlorination bacteria (CORB). Even though methanogenesis frequently occurs during dechlorination of organic chlorinated pollutants (OCPs) in situ, the underestimated effect of methanogens and their interactions with dechlorinators remains unknown. We investigated the association between dechlorination and methanogenesis, as well as the performance of methanogens involved in reductive dechlorination, through the use of meta-analysis, incubation experiment, untargeted metabolomic analysis, and thermodynamic modeling approaches. The meta-analysis indicated that methanogenesis is largely synchronously associated with OCP dechlorination, that OHRB are not the sole degradation engineers that maintain OCP bioremediation, and that methanogens are fundamentally needed to sustain microenvironment functional balance. Laboratory results further confirmed that Methanosarcina barkeri (M. barkeri) promotes the dechlorination of γ-hexachlorocyclohexane (γ-HCH). Untargeted metabolomic analysis revealed that the application of γ-HCH upregulated the metabolic functioning of chlorocyclohexane and chlorobenzene degradation in M. barkeri, further confirming that M. barkeri potentially possesses an auxiliary dechlorination function. Finally, quantum analysis based on density functional theory (DFT) indicated that the methanogenic coenzyme F430 significantly reduces the activation barrier to dechlorination. Collectively, this work suggests that methanogens are highly involved in microbial reductive dechlorination at OCP-contaminated sites and may even directly favor OCP degradation.

Methane-associated micro-ecological processes crucially improve the self-purification of lindane-polluted paddy soil

Reductive dechlorination, an efficient pathway for complete removal of organic chlorinated pollutants (OCPs), is commonly reported to be coupled to oxidation of methane (CH₄) or methanogenesis in anaerobic environments. However, the relationship between dechlorination and CH₄-associated bioprocesses is unclear. Based on the hypothesis that CH₄ supplementation could facilitate OCP dechlorination, we investigated the role of CH₄-associated bioprocesses in the self-purification of flooded lindane-spiked paddy soils. Four treatments were conducted for up to 28 days: sterilized soil (S), sterilized soil + CH₄ (SC), non-sterilized soil (NS), and non-sterilized soil + CH₄ (NSC). Results indicated that both sterilization and addition of CH₄ promoted lindane degradation and CH₄ emissions in the flooded paddy soils. In the NS treatment, lindane had the lowest degradation rate when CH₄ emissions were barely detected; while in the SC treatment, lindane had the highest degradation rate when CH₄ achieved its highest emissions from anaerobic soil. Also, sterilization led to microbial diversity loss and functional recession, but increased ferrous ion [Fe(II)] concentrations compared to non-sterilized soils. Methanogenic communities and mcrA gene recovered faster than the majority of microorganisms (e.g., Fe bacteria, Bdellovibrionaceae, Rhizobiaceae, Dehalogenimonas) or functional genes (e.g., Dhc, Geo, narG, nirS). Collectively, we assume the enhanced removal of lindane may partly be due to both abiotic dechlorination promoted by chemical Fe redox processes and methanogenesis-derived biotic dechlorination. Revealing the coupling between dechlorination and CH₄-associated bioprocesses is helpful to resolve both pollution remediation and mitigation of CH₄ emissions in anaerobic contaminated sites.

How do phytogenic iron oxide nanoparticles drive redox reactions to reduce cadmium availability in a flooded paddy soil?

While soil redox reactions are known to determine heavy metal soil availability, specific information on how iron (Fe) nanomaterials reduce heavy metal availability in bulk soil and in the rice rhizosphere is limited. Here a pot experiment was performed to examine the effect of phytogenic iron oxide nanoparticles (PION) on the availability of cadmium (Cd) in flooded soil. PION significantly reduced soil Cd availability, with Cd in rice shoot being 2.72, 1.21 and 0.40 mg kg^-1 for the control, 1 and 5% PION treatments, respectively. In addition, following PION application, Illumina MiSeq sequencing indicated that the abundance of Lentimicrobium and Anaeromyxobacter increased, while the abundance of Geobacter and Thiobacillus decreased. Structural equation model analysis revealed that redox reactions, driven by carbon, nitrogen, iron and sulfur cycling related functional groups, played an important role in the immobilization of Cd in flooded soil. Co-occurrence network analysis showed that the rhizosphere soil was far more complex than the bulk soil. Overall, PION addition enhanced the inherent soil microbe's activity and the involved in reducing Cd availability to rice by converting mobile Cd into stabler forms. This initial result paves the way for establishing a practical low-cost remediation strategy for Cd contaminated paddy soils.

Nanoscale zero-valent iron reduction coupled with anaerobic dechlorination to degrade hexachlorocyclohexane isomers in historically contaminated soil

Hexachlorocyclohexane (HCH) isomers pose potential threats to the environment and to public health due to their persistence and high toxicity. In this study, nanoscale zero-valent iron (nZVI) coupled with microbial degradation by indigenous microorganisms with and without biostimulation was employed to remediate soils highly polluted with HCH. The degradation efficiency of total HCHs in both the "nZVI-only" and "Non-amendment" treatments was approximately 50 %, while in the treatment amended with nZVI and acetate, 85 % of total HCHs was removed. Addition of nZVI and acetate resulted in enrichment of anaerobic microorganisms. The results of quantitative PCR (qPCR) and 16S rRNA gene amplicon sequencing revealed that Desulfotomaculum, Dehalobacter, Geobacter, and Desulfuromonas likely contributed to the depletion of HCH isomers. Moreover, some abiotic factors also favored this removal process, including pH, and the generation of iron sulfides as revealed by the result of Mössbauer spectrometer analysis. Our research provides an improved remediation strategy for soils polluted with HCH isomers and an understanding of the synergistic effect of nZVI and indigenous microorganisms.

Metagenomic Insights into Rhizospheric Microbiome Profiling in Lentil Cultivars Unveils Differential Microbial Nitrogen and Phosphorus Metabolism under Rice-Fallow Ecology

The plant rhizosphere interfaces an array of microbiomes related to plant growth and development. Cultivar-specific soil microbial communities with respect to their taxonomic structure and specific function have not been investigated explicitly in improving the adaptation of lentil cultivars under rice-fallow ecology. The present study was carried out to decipher the rhizosphere microbiome assembly of two lentil cultivars under rice-fallow ecology for discerning the diversity of microbial communities and for predicting the function of microbiome genes related to nitrogen (N) and phosphorus (P) cycling processes deploying high-throughput whole (meta) genome sequencing. The metagenome profile of two cultivars detected variable microbiome composition with discrete metabolic activity. Cyanobacteria, Bacteroidetes, Proteobacteria, Gemmatimonadetes, and Thaumarchaeota were abundant phyla in the “Farmer-2” rhizosphere, whereas Actinobacteria, Acidobacteria, Firmicutes, Planctomycetes, Chloroflexi, and some incompletely described procaryotes of the “Candidatus” category were found to be robustly enriched the rhizosphere of “Moitree”. Functional prediction profiles of the microbial metagenomes between two cultivars revealed mostly house keeping genes with general metabolism. Additionally, the rhizosphere of “Moitree” had a high abundance of genes related to denitrification processes. Significant difference was observed regarding P cycling genes between the cultivars. “Moitree” with a profuse root system exhibited better N fixation and translocation ability due to a good “foraging strategy” for improving acquisition of native P under the nutrient depleted rice-fallow ecology. However, “Farmer-2” revealed a better “mining strategy” for enhancing P solubilization and further transportation to sinks. This study warrants comprehensive research for explaining the role of microbiome diversity and cultivar–microbe interactions towards stimulating microbiome-derived soil reactions regarding nutrient availability under rice-fallow ecology.

Pollution adaptive responses of root-associated microbiomes induced the promoted but different attenuation of soil residual lindane: Differences between maize and soybean

Microorganisms colonize plant-associated environments and constitute complex communities aided in key functions for nutrient acquisition, disease suppression and abiotic stress resistance. In this study, we evaluated the variation of root-associated microbiomes of two typical farmland crops, maize (Zea mays L.) and soybean (Glycine max L. Merr.) respond to organochlorine pesticide stress, taking lindane as an example. Results showed that there were promoted but different attenuation rates of residual lindane in rhizosphere soils during maize and soybean growth, and the differential is due to the comprehensive effects of plant characters and microbial activities. Organochlorine pollution did not have significant impact on the microbial diversity and populations in all rhizo-compartments, but mostly stimulated the microbial connectivity. The multistep and decreasing processes for root-associated microbiomes of both maize and soybean were spatially different and mainly dependent on the shaping roles of host plants. These results expand our understandings of the organochlorine influence on the underground ecological system in crop-dependent soils.

Sub-Lethal Effects of Pesticides on the DNA of Soil Organisms as Early Ecotoxicological Biomarkers

This review describes the researches performed in the last years to assess the impact of pesticide sub-lethal doses on soil microorganisms and non-target organisms in agricultural soil ecosystems. The overview was developed through the careful description and a critical analysis of three methodologies based on culture-independent approaches involving DNA extraction and sequencing (denaturing gradient gel electrophoresis, DGGE; next-generation sequencing, NGS) to characterize the microbial population and DNA damage assessment (comet assay) to determine the effect on soil invertebrates. The examination of the related published articles showed a continuous improvement of the possibility to detect the detrimental effect of the pesticides on soil microorganisms and non-target organisms at sub-lethal doses, i.e., doses which have no lethal effect on the organisms. Considering the overall critical discussion on microbial soil monitoring in the function of pesticide treatments, we can confirm the usefulness of PCR-DGGE as a screening technique to assess the genetic diversity of microbial communities. Nowadays, DGGE remains a preliminary technique to highlight rapidly the main differences in microbial community composition, which is able to give further information if coupled with culture-dependent microbiological approaches, while thorough assessments must be gained by high-throughput techniques such as NGS. The comet assay represents an elective technique for assessing genotoxicity in environmental biomonitoring, being mature after decades of implementation and widely used worldwide for its direct, simple, and affordable implementation. Nonetheless, in order to promote the consistency and reliability of results, regulatory bodies should provide guidelines on the optimal use of this tool, strongly indicating the most reliable indicators of DNA damage. This review may help the European Regulation Authority in deriving new ecotoxicological endpoints to be included in the Registration Procedure of new pesticides.

Phytoremediation of pharmaceutical-contaminated wastewater: Insights into rhizobacterial dynamics related to pollutant degradation mechanisms during plant life cycle

Rhizobacterial dynamics, relating to pollutant degradation mechanisms, over the course of plant lifespan have rarely been reported when using phytoremediation technologies for pharmaceutical-contaminated wastewater treatment. This study investigated the rhizobacterial dynamics of Typha angustifolia in constructed wetlands to treat ibuprofen (IBP)-polluted wastewater throughout plant development from seedling, vegetative, bolting, mature, to senescent stages. It was found that conventional pollutant and IBP removals increased with plant development, reaching to the best performance at bolting or mature stage (removal efficiencies: 92% organics, 52% ammonia, 60% phosphorus and 76% IBP). In the IBP-stressed wetlands, the rhizobacterial diversity during plant development was adversely affected by IBP accompanied with a reduced evenness. The bacterial communities changed dynamically at different developmental stages and showed significant differences compared to the control wetlands (free of IBP). The dominant bacteria colonized in the rhizosphere was the phylum Actinobacteria, having a final relative abundance of 0.79 and containing a large amount of genus norank_o__PeM15. Positive interactions were evident among the rhizobacteria in IBP-stressed wetlands and the predicted functions of 16S rRNA genes revealed the potential co-metabolism and metabolism of IBP. The co-metabolism of IBP might be related to root exudates such as amino acid, lipid, fatty acid and organic acid. In addition, positive correlations between the organic compounds of interstitial water (bulk environment) and the rhizobacterial communities were observed in IBP-stressed wetlands, which suggests that the influence of IBP on bulk microbiome might be able to modulate rhizosphere microbiome to achieve the degradation of IBP via co-metabolism or metabolism.

Novel cultivated endophytic Verrucomicrobia reveal deep-rooting traits of bacteria to associate with plants

Despite the relevance of complex root microbial communities for plant health, growth and productivity, the molecular basis of these plant-microbe interactions is not well understood. Verrucomicrobia are cosmopolitans in the rhizosphere, nevertheless their adaptations and functions are enigmatic since the proportion of cultured members is low. Here we report four cultivated Verrucomicrobia isolated from rice, putatively representing four novel species, and a novel subdivision. The aerobic strains were isolated from roots or rhizomes of Oryza sativa and O. longistaminata. Two of them are the first cultivated endophytes of Verrucomicrobia, as validated by confocal laser scanning microscopy inside rice roots after re-infection under sterile conditions. This extended known verrucomicrobial niche spaces. Two strains were promoting root growth of rice. Discovery of root compartment-specific Verrucomicrobia permitted an across-phylum comparison of the genomic conformance to life in soil, rhizoplane or inside roots. Genome-wide protein domain comparison with niche-specific reference bacteria from distant phyla revealed signature protein domains which differentiated lifestyles in these microhabitats. Our study enabled us to shed light into the dark microbial matter of root Verrucomicrobia, to define genetic drivers for niche adaptation of bacteria to plant roots, and provides cultured strains for revealing causal relationships in plant-microbe interactions by reductionist approaches.

Dynamic processes in conjunction with microbial response to disclose the biochar effect on pentachlorophenol degradation under both aerobic and anaerobic conditions

Organochlorines are critical soil contaminants and the use of biochar has recently shown potential to improve soil remediation. However, little is known about biochar-microbe interactions nor the impact on environmental processes such as the immobilization and biodegradation of organochlorine compounds. In this study, we performed microcosm experiments to elucidate how biochar affected the biodegradation and sequestration of pentachlorophenol (PCP). Our results showed that the amendment of biochar markedly inhibited PCP biodegradation due to a strong sorption affinity for PCP under both aerobic and anaerobic conditions. Notably, the inhibitory effect was relatively weaker under anaerobic conditions than under aerobic conditions. The addition of biochar can dramatically shift the bacterial community diversity in the PCP-spiked soils. Under aerobic conditions, biochar significantly stimulated the growth of PCP-degrading bacteria Bacillus and Sphingomonas, but reduced the opportunities for microbes to contact with PCP directly. Under anaerobic conditions, the non-strict organohalide-respiring bacteria Desulfovibrio, Anaeromyxobacter, Geobacter and Desulfomonile were the main drivers of PCP transformation. Our results imply that the use of biochar as a soil remediation strategy for organochlorine compounds should be cautious.