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Background: Given the increasing exposure of humans to environmental chemicals and the limitations of conventional toxicity test, there is an urgent need to develop next-generation risk assessment methods., Objectives: This study aims to establish a novel computational system named Toxicogenomics Scoring System (TGSS) to predict the carcinogenicity of chemicals coupling chemical-gene interactions with multiple cancer transcriptomic datasets., Methods: Chemical-related gene signatures were derived from chemical-gene interaction data from the Comparative Toxicogenomics Database (CTD). For each cancer type in TCGA, genes were ranked by their effects on tumorigenesis, which is based on the differential expression between tumor and normal samples. Next, we developed carcinogenicity scores (C-scores) using pre-ranked GSEA to quantify the correlation between chemical-related gene signatures and ranked gene lists. Then we established TGSS by systematically evaluating the C-scores in multiple chemical-tumor pairs. Furthermore, we examined the performance of our approach by ROC curves or prognostic analyses in TCGA and multiple independent cancer cohorts., Results: Forty-six environmental chemicals were finally included in the study. C-score was calculated for each chemical-tumor pair. The C-scores of IARC Group 3 chemicals were significantly lower than those of chemicals in Group 1 (P-value = 0.02) and Group 2 (P-values = 7.49 ×10 -5 ). ROC curves analysis indicated that C-score could distinguish "high-risk chemicals" from the other compounds (AUC = 0.67) with a specificity and sensitivity of 0.86 and 0.57. The results of survival analysis were also in line with the assessed carcinogenicity in TGSS for the chemicals in Group 1. Finally, consistent results were further validated in independent cancer cohorts., Conclusion: TGSS highlighted the great potential of integrating chemical-gene interactions with gene-cancer relationships to predict the carcinogenic risk of chemicals, which would be valuable for systems toxicology., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)

Soil fungi are key drivers in regulating the ecosystem function, playing a vital role in protecting the plant from phytopathogens and other biotic and abiotic pressures. However, the potential impact of compost addition and soil aggregate size on the fungal community and functional ecological guild remains uncertain. This study investigated the structure, composition, and function of soil fungal communities across aggregate fractions under food waste compost addition using Miseq sequencing and FUNGuild. Compost addition exerted a negative impact on fungal α-diversity, and shifted the structure and changed the composition of fungal community. Compost addition rates exhibited more contributions to fungal α-diversity variations (R = 0.609, 0.895, and 0.501 for Sobs, Shannon, and Chao indices, respectively, P = 0.001) and the separation of community structure than soil aggregate size (R = 0.952, P = 0.001). Biomarkers, including Chaetomiaceae, Ascobolaceae, and Sordariomycete, displayed significant superiority in compost-added soils, whereas the populations of Nectriaceae and Clavicipitaceae were significantly decreased. The relative abundances of animal and plant pathogens were significantly decreased, whereas that of saprotrophs were increased. The abundances of pathogens correlated positively with pH and negatively with nutrients (soil organic matter, dissolved organic carbon, total nitrigen, NH 4 + , and NO 3 - ), whereas those of saprotrophs showed an opposite trend. The dose of compost was the major driver for fungal functional guild variation, whereas carbon and nitrogen source exhibited more contributions to function variation than pH value. These results provide a reference for sustainable ecological agriculture by applying compost rationally under the conditions of soil health and agricultural performance., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021. Published by Elsevier B.V.)

Irrigation with treated wastewater (TWW) influences soil ecological function due to the accumulation of heavy metals (HMs) and nutrients in soils. However, the interaction between HMs and microbial processes in TWW-irrigated soil has not been fully explored. We investigated the effect of HMs on bacterial communities and nitrogen-transforming (N-transforming) genes along vertical soil profiles irrigated with domestic TWW (DTWW) and industrial TWW (ITWW) for more than 30 years. Results indicate that long-term TWW irrigation reshaped bacterial community structure and composition. Irrigation with ITWW led to increased accumulation of Cd, Cr, Cu, Pb, Zn, and Ni in soils than DTWW. Accumulation of inorganic N, soil organic carbon, and HMs in topsoil irrigated with ITWW contributed to the activities of Micrococcaceae. The effect of the activation of nutrient factors on Bacillus, which was the dominant species in DTWW-irrigated soils, was greater than that of HMs. HM pressure driven by ITWW irrigation changed the vertical distribution of N-transforming functional genes, increasing the abundance of amoA gene and decreasing that of nifH through soil depth. ITWW irrigation enhanced the denitrification capacity in topsoil; ammonia-oxidizing capacity in deeper soil was increased after long-term irrigation with DTWW and ITWW, suggesting a potential risk of nitrogen loss., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Microplastics can alter the physicochemical and biogeochemical processes in soil, but whether these alterations have further the effects on the transformation of soil heavy metal speciation, and if so, whether these effects vary across soil aggregate levels remain unknown. Herein, long-term soil culture experiments and soil fractionation are combined to investigate the effects of microplastics on chemical speciation of Cu, Cr, and Ni with different particle-size soil aggregates. Results show that microplastics in soil decrease the exchangeable, carbonate-bound, and Fe-Mn oxide-bound fractions of metals but increase their organic-bound fractions via direct adsorption and indirect effects on the soil microenvironment conditions. The findings suggest that microplastics can promote the transformation of heavy metal speciation from bioavailable to organic bound. Such promotion exerts notable differences across soil aggregate levels. The transformation of soil heavy metal speciation is greater in larger aggregates than in smaller aggregates in the early incubation period with microplastics but shows the opposite trend in the later incubation period. Therefore, this process is more sensitive to long-term microplastic pollution in smaller aggregates than in larger aggregates, most likely owing to the lag in the influence of microplastics on metal speciation transformation in the smaller aggregates., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier B.V. All rights reserved.)

A significant fraction of humic substances (HS) in natural soils is protected due to the interactions with mineral surfaces or occlusion within aggregates and clay microstructures, which could render the solid-phase HS less spatially accessible to microorganisms and thus affect their extracellular electron transfer. However, more diverse and convincing evidence is needed to further verify the link between extracellular electron transfer of solid-phase HS and their physico-chemical protection mechanisms in soils. In this study, soil physical fractionation and mediated electrochemical measurements were combined for the first time to assess the microbially reducible extents of solid-phase HS in mineral soils. The results show that the solid-phase HS in soil contain several pools with different microbially reducible extents, due to the fact that different pools employ distinct protection mechanisms of soil organic matter against microbial attacks; the particulate HS exert the greatest microbially reducible extent, followed by the microaggregate occluded HS and non-aggregated silt associated HS, and non-aggregated clay associated HS exert the lowest microbially reducible extent. Our work provides a new evidence to validate the view that the extracellular electron transfer process of solid-phase HS in natural soils is largely controlled by their physico-chemical protection mechanisms., (Copyright © 2019 Elsevier B.V. All rights reserved.)

The microbial reduction of Fe(III) minerals (MRF) is an important process in paddy soil because it can affect the biogeochemical cycles of many major and trace elements. Natural organic matter (NOM) that mainly exists in the form of solid phase in soil can mediate MRF through electron shuttling functionality. However, whether a link exists between solid-phase NOM-mediated MRF in soil and the age of paddy field since the reclamation on fallow is unclear. Here, we use microbial reduction method to assess the solid-phase NOM-mediated MRF of paddy soils with different reclamation ages. The results show that solid-phase NOM-mediated MRF exhibits a positive response to land use change sequence from fallow to paddy field, indicating that the long-term natural development of paddy field favors the electron shuttling of NOM between cells and Fe(III) minerals. This increase in the electron shuttling of NOM is not due to the increase in the redox functional groups of NOM, but may be attributed to the formation of NOM-mineral complex through the synergistic increases in NOM content and transformation of soil texture from clay loam to loam. The decrease in the redox potential of Fe(III) minerals in soil caused by decreased pH and the increase in Fe content in the organic matter-complexed form may also partly facilitate electron transfer from NOM to Fe(III) minerals. Our work is useful in predicting the role of soil solid-phase NOM in mediating MRF in the context of long-term reclamation of paddy field and provides guidance for the environmental management of paddy fields., (Copyright © 2019 Elsevier B.V. All rights reserved.)